Starting phenix.real_space_refine
on Fri Aug 22 12:40:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jga_36228/08_2025/8jga_36228.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jga_36228/08_2025/8jga_36228.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jga_36228/08_2025/8jga_36228.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jga_36228/08_2025/8jga_36228.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jga_36228/08_2025/8jga_36228.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jga_36228/08_2025/8jga_36228.map"
  }
  resolution = 3.68
  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=   0.002 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       7      5.16       5
     C     987      2.51       5
     N     249      2.21       5
     O     273      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 1516
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1516
          Classifications: {'peptide': 202}
          Incomplete info: {'backbone_only': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 191}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 0.74, per 1000 atoms: 0.49
  Number of scatterers: 1516
  At special positions: 0
  Unit cell: (54.78, 50.63, 55.61, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       7     16.00
     O     273      8.00
     N     249      7.00
     C     987      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 165 " - pdb=" SG  CYS A 203 " distance=2.03

  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: 0.13
  Conformation dependent library (CDL) restraints added in 65.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  362

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 3 sheets defined
      58.4% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
    Processing helix  chain 'A' and resid 20 through 35
      removed outlier: 3.506A  pdb=" N   LEU A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ALA A  30 " --> pdb=" O   LYS A  26 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL A  31 " --> pdb=" O   LYS A  27 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   PHE A  32 " --> pdb=" O   ALA A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 56
    Processing helix  chain 'A' and resid 56 through 62
      removed outlier: 4.314A  pdb=" N   GLU A  60 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   MET A  61 " --> pdb=" O   PHE A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 82
    Processing helix  chain 'A' and resid 93 through 104
    Processing helix  chain 'A' and resid 113 through 124
      removed outlier: 4.002A  pdb=" N   LYS A 119 " --> pdb=" O   THR A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 137
    Processing helix  chain 'A' and resid 137 through 145
      removed outlier: 4.100A  pdb=" N   VAL A 141 " --> pdb=" O   GLY A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 169
    Processing helix  chain 'A' and resid 185 through 202
      removed outlier: 3.799A  pdb=" N   ALA A 190 " --> pdb=" O   PRO A 186 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   GLU A 191 " --> pdb=" O   VAL A 187 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLU A 198 " --> pdb=" O   LYS A 194 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   LYS A 199 " --> pdb=" O   ALA A 195 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ILE A 200 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ARG A 201 " --> pdb=" O   VAL A 197 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 15
      removed outlier: 6.254A  pdb=" N   ALA A  14 " --> pdb=" O   GLU A  40 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   THR A  42 " --> pdb=" O   ALA A  14 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88
      removed outlier: 3.553A  pdb=" N   MET A 108 " --> pdb=" O   ILE A  87 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 129
      removed outlier: 6.784A  pdb=" N   LEU A 128 " --> pdb=" O   VAL A 154 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3

    65 hydrogen bonds defined for protein.
    195 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.21

  Time building geometry restraints manager: 0.17 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: 381
        1.33 -     1.46: 306
        1.46 -     1.58: 846
        1.58 -     1.71: 0
        1.71 -     1.83: 12
  Bond restraints: 1545
  Sorted by residual:
  bond pdb=" C   LYS A 183 "
       pdb=" O   LYS A 183 "
    ideal  model  delta    sigma   weight residual
    1.234  1.207  0.026 1.19e-02 7.06e+03 4.92e+00
  bond pdb=" C   LEU A 181 "
       pdb=" O   LEU A 181 "
    ideal  model  delta    sigma   weight residual
    1.235  1.213  0.022 1.26e-02 6.30e+03 3.15e+00
  bond pdb=" C   VAL A 182 "
       pdb=" O   VAL A 182 "
    ideal  model  delta    sigma   weight residual
    1.236  1.218  0.018 1.19e-02 7.06e+03 2.36e+00
  bond pdb=" CA  LYS A 183 "
       pdb=" C   LYS A 183 "
    ideal  model  delta    sigma   weight residual
    1.525  1.506  0.020 1.29e-02 6.01e+03 2.31e+00
  bond pdb=" CG  LEU A 173 "
       pdb=" CD1 LEU A 173 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.61e+00
  ... (remaining 1540 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 1985
        1.63 -     3.27: 76
        3.27 -     4.90: 19
        4.90 -     6.54: 2
        6.54 -     8.17: 2
  Bond angle restraints: 2084
  Sorted by residual:
  angle pdb=" C   LYS A 183 "
        pdb=" N   GLY A 184 "
        pdb=" CA  GLY A 184 "
      ideal   model   delta    sigma   weight residual
     121.23  125.06   -3.83 1.34e+00 5.57e-01 8.16e+00
  angle pdb=" N   ALA A 180 "
        pdb=" CA  ALA A 180 "
        pdb=" C   ALA A 180 "
      ideal   model   delta    sigma   weight residual
     112.59  109.52    3.07 1.22e+00 6.72e-01 6.33e+00
  angle pdb=" C   ASN A  19 "
        pdb=" N   SER A  20 "
        pdb=" CA  SER A  20 "
      ideal   model   delta    sigma   weight residual
     121.54  126.00   -4.46 1.91e+00 2.74e-01 5.46e+00
  angle pdb=" CA  LEU A  55 "
        pdb=" CB  LEU A  55 "
        pdb=" CG  LEU A  55 "
      ideal   model   delta    sigma   weight residual
     116.30  124.47   -8.17 3.50e+00 8.16e-02 5.45e+00
  angle pdb=" C   VAL A 164 "
        pdb=" N   CYS A 165 "
        pdb=" CA  CYS A 165 "
      ideal   model   delta    sigma   weight residual
     121.58  117.20    4.38 1.95e+00 2.63e-01 5.04e+00
  ... (remaining 2079 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    15.82: 821
       15.82 -    31.64: 81
       31.64 -    47.46: 22
       47.46 -    63.28: 7
       63.28 -    79.10: 1
  Dihedral angle restraints: 932
    sinusoidal: 368
      harmonic: 564
  Sorted by residual:
  dihedral pdb=" CB  CYS A 165 "
           pdb=" SG  CYS A 165 "
           pdb=" SG  CYS A 203 "
           pdb=" CB  CYS A 203 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   42.70   50.30     1      1.00e+01 1.00e-02 3.47e+01
  dihedral pdb=" CA  LYS A 152 "
           pdb=" C   LYS A 152 "
           pdb=" N   PHE A 153 "
           pdb=" CA  PHE A 153 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.76  -17.24     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  GLY A 202 "
           pdb=" C   GLY A 202 "
           pdb=" N   CYS A 203 "
           pdb=" CA  CYS A 203 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.98  -17.02     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 929 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 139
       0.039 -    0.079: 66
       0.079 -    0.118: 30
       0.118 -    0.157: 8
       0.157 -    0.197: 1
  Chirality restraints: 244
  Sorted by residual:
  chirality pdb=" CG  LEU A 181 "
            pdb=" CB  LEU A 181 "
            pdb=" CD1 LEU A 181 "
            pdb=" CD2 LEU A 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 9.66e-01
  chirality pdb=" CA  PRO A 186 "
            pdb=" N   PRO A 186 "
            pdb=" C   PRO A 186 "
            pdb=" CB  PRO A 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.66e-01
  chirality pdb=" CA  ILE A  64 "
            pdb=" N   ILE A  64 "
            pdb=" C   ILE A  64 "
            pdb=" CB  ILE A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.47e-01
  ... (remaining 241 not shown)

  Planarity restraints: 263
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 185 "    0.030 5.00e-02 4.00e+02   4.49e-02 3.23e+00
        pdb=" N   PRO A 186 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 186 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 186 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 108 "    0.029 5.00e-02 4.00e+02   4.42e-02 3.13e+00
        pdb=" N   PRO A 109 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 109 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 109 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 183 "    0.007 2.00e-02 2.50e+03   1.40e-02 1.95e+00
        pdb=" C   LYS A 183 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   LYS A 183 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLY A 184 "    0.008 2.00e-02 2.50e+03
  ... (remaining 260 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 254
        2.76 -     3.30: 1514
        3.30 -     3.83: 2527
        3.83 -     4.37: 2950
        4.37 -     4.90: 5061
  Nonbonded interactions: 12306
  Sorted by model distance:
  nonbonded pdb=" O   ASP A  49 "
            pdb=" OG  SER A  82 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OG  SER A  89 "
            pdb=" OH  TYR A 107 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OG1 THR A 126 "
            pdb=" O   ASN A 150 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OG  SER A  97 "
            pdb=" NE2 HIS A 125 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" NZ  LYS A  27 "
            pdb=" O   GLY A 184 "
     model   vdw
     2.383 3.120
  ... (remaining 12301 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             8.530
  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:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.110
  Find NCS groups from input model:        0.000
  Set up NCS constraints:                  0.000
  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:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
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      :  0.005   0.042   1546  Z= 0.229
  Angle     :  0.812   8.171   2086  Z= 0.452
  Chirality :  0.054   0.197    244
  Planarity :  0.006   0.045    263
  Dihedral  : 14.340  79.102    567
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 16.80
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  7.00 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  0.62 %
    Favored  : 98.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -2.18 (0.60), residues: 200
  helix: -1.12 (0.51), residues: 108
  sheet: -1.53 (0.88), residues: 30
  loop : -1.61 (0.84), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.002   ARG A  77 
 TYR   0.005   0.001   TYR A 107 
 PHE   0.017   0.002   PHE A  99 
 TRP   0.002   0.001   TRP A 167 
 HIS   0.002   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 1545)
  covalent geometry    : angle       0.81114 ( 2084)
  SS BOND              : bond        0.00381 (    1)
  SS BOND              : angle       1.64538 (    2)
  hydrogen bonds       : bond        0.10055 (   65)
  hydrogen bonds       : angle       7.20795 (  195)

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 26
  time to evaluate  : 0.062 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 28
  average time/residue: 0.0941
  time to fit residues: 2.9134
Evaluate side-chains
  21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   chunk 9 optimal weight:    8.9990
   chunk 11 optimal weight:    0.0060
   chunk 18 optimal weight:    0.0000
   chunk 6 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.5804

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

Flipped N/Q/H residues before XYZ refinement:
A 150 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.118679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.104429 restraints weight = 2116.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.107417 restraints weight = 1259.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.109516 restraints weight = 858.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.110922 restraints weight = 634.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.111993 restraints weight = 507.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.1259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   1546  Z= 0.121
  Angle     :  0.690   9.720   2086  Z= 0.337
  Chirality :  0.048   0.130    244
  Planarity :  0.005   0.046    263
  Dihedral  :  5.749  27.191    209
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 10.56 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.94 (0.61), residues: 200
  helix: -0.97 (0.51), residues: 108
  sheet: -1.24 (0.95), residues: 30
  loop : -1.52 (0.83), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  17 
 TYR   0.006   0.001   TYR A 107 
 PHE   0.009   0.001   PHE A  43 
 TRP   0.007   0.002   TRP A 167 
 HIS   0.001   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 1545)
  covalent geometry    : angle       0.68917 ( 2084)
  SS BOND              : bond        0.00325 (    1)
  SS BOND              : angle       1.35769 (    2)
  hydrogen bonds       : bond        0.03021 (   65)
  hydrogen bonds       : angle       5.97376 (  195)

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 21
  time to evaluate  : 0.073 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 23
  average time/residue: 0.0897
  time to fit residues: 2.3127
Evaluate side-chains
  23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  183 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 18 optimal weight:    0.0030
   chunk 3 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   overall best weight:    1.3394

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.108228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.090983 restraints weight = 2157.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.094141 restraints weight = 1300.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.096416 restraints weight = 903.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.098021 restraints weight = 683.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.099286 restraints weight = 550.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   1546  Z= 0.137
  Angle     :  0.657   9.010   2086  Z= 0.322
  Chirality :  0.048   0.135    244
  Planarity :  0.005   0.044    263
  Dihedral  :  5.605  29.645    209
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 14.91 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.72 (0.61), residues: 200
  helix: -0.77 (0.51), residues: 109
  sheet: -1.26 (0.96), residues: 30
  loop : -1.39 (0.86), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  17 
 TYR   0.004   0.001   TYR A 107 
 PHE   0.021   0.002   PHE A  32 
 TRP   0.005   0.001   TRP A 167 
 HIS   0.001   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 1545)
  covalent geometry    : angle       0.65576 ( 2084)
  SS BOND              : bond        0.00346 (    1)
  SS BOND              : angle       1.34512 (    2)
  hydrogen bonds       : bond        0.02920 (   65)
  hydrogen bonds       : angle       5.65162 (  195)

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 19
  time to evaluate  : 0.061 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 21
  average time/residue: 0.0880
  time to fit residues: 2.0745
Evaluate side-chains
  22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 18
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  183 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 9 optimal weight:    0.6980
   chunk 13 optimal weight:    0.4980
   chunk 8 optimal weight:    8.9990
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.9982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.121682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.107416 restraints weight = 2115.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.110308 restraints weight = 1299.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.112132 restraints weight = 909.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.113539 restraints weight = 698.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.114627 restraints weight = 565.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   1546  Z= 0.115
  Angle     :  0.603   8.257   2086  Z= 0.299
  Chirality :  0.047   0.135    244
  Planarity :  0.005   0.042    263
  Dihedral  :  5.341  29.612    209
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 16.15 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.55 (0.62), residues: 200
  helix: -0.56 (0.52), residues: 109
  sheet: -1.24 (0.96), residues: 30
  loop : -1.45 (0.84), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  77 
 TYR   0.003   0.001   TYR A 107 
 PHE   0.015   0.002   PHE A  32 
 TRP   0.006   0.002   TRP A 167 
 HIS   0.001   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 1545)
  covalent geometry    : angle       0.60200 ( 2084)
  SS BOND              : bond        0.00336 (    1)
  SS BOND              : angle       1.25203 (    2)
  hydrogen bonds       : bond        0.02746 (   65)
  hydrogen bonds       : angle       5.39154 (  195)

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.070 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 25
  average time/residue: 0.0630
  time to fit residues: 1.8455
Evaluate side-chains
  23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  183 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 11 optimal weight:    0.2980
   chunk 9 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.2186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.108902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.091995 restraints weight = 2134.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.095057 restraints weight = 1295.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.097255 restraints weight = 903.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.098838 restraints weight = 685.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.100107 restraints weight = 552.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   1546  Z= 0.127
  Angle     :  0.622   6.868   2086  Z= 0.309
  Chirality :  0.047   0.136    244
  Planarity :  0.005   0.041    263
  Dihedral  :  5.238  28.706    209
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 17.39 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.45 (0.62), residues: 200
  helix: -0.51 (0.52), residues: 109
  sheet: -1.20 (0.96), residues: 30
  loop : -1.35 (0.86), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  77 
 TYR   0.003   0.001   TYR A 107 
 PHE   0.011   0.001   PHE A  32 
 TRP   0.004   0.001   TRP A 167 
 HIS   0.001   0.001   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 1545)
  covalent geometry    : angle       0.62106 ( 2084)
  SS BOND              : bond        0.00317 (    1)
  SS BOND              : angle       1.21352 (    2)
  hydrogen bonds       : bond        0.02792 (   65)
  hydrogen bonds       : angle       5.25305 (  195)

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.063 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 21
  average time/residue: 0.0647
  time to fit residues: 1.5883
Evaluate side-chains
  22 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 19
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  183 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 2 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.119592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.106108 restraints weight = 2108.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.108725 restraints weight = 1276.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.110660 restraints weight = 886.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.112060 restraints weight = 666.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.112940 restraints weight = 533.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   1546  Z= 0.114
  Angle     :  0.598   6.539   2086  Z= 0.297
  Chirality :  0.046   0.135    244
  Planarity :  0.004   0.040    263
  Dihedral  :  5.093  28.072    209
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 19.88 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.34 (0.63), residues: 200
  helix: -0.45 (0.53), residues: 109
  sheet: -1.06 (0.93), residues: 32
  loop : -1.27 (0.88), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  77 
 TYR   0.003   0.001   TYR A 107 
 PHE   0.011   0.002   PHE A  32 
 TRP   0.005   0.002   TRP A 167 
 HIS   0.001   0.000   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 1545)
  covalent geometry    : angle       0.59768 ( 2084)
  SS BOND              : bond        0.00314 (    1)
  SS BOND              : angle       1.15905 (    2)
  hydrogen bonds       : bond        0.02708 (   65)
  hydrogen bonds       : angle       5.13456 (  195)

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 22
  time to evaluate  : 0.057 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 24
  average time/residue: 0.0588
  time to fit residues: 1.6281
Evaluate side-chains
  21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  115 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 6 optimal weight:    9.9990
   chunk 13 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    0.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.123486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.109502 restraints weight = 2047.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.112163 restraints weight = 1236.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.114172 restraints weight = 862.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.115546 restraints weight = 653.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.116363 restraints weight = 522.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   1546  Z= 0.112
  Angle     :  0.594   6.023   2086  Z= 0.294
  Chirality :  0.047   0.134    244
  Planarity :  0.004   0.038    263
  Dihedral  :  4.605  13.902    205
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 22.98 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.24 (0.62), residues: 200
  helix: -0.37 (0.53), residues: 109
  sheet: -1.02 (0.91), residues: 32
  loop : -1.21 (0.87), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A  77 
 TYR   0.002   0.001   TYR A 107 
 PHE   0.011   0.001   PHE A  32 
 TRP   0.007   0.002   TRP A 167 
 HIS   0.001   0.000   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 1545)
  covalent geometry    : angle       0.59323 ( 2084)
  SS BOND              : bond        0.00289 (    1)
  SS BOND              : angle       1.11067 (    2)
  hydrogen bonds       : bond        0.02671 (   65)
  hydrogen bonds       : angle       5.03566 (  195)

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 18
  time to evaluate  : 0.066 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 19
  average time/residue: 0.0538
  time to fit residues: 1.2330
Evaluate side-chains
  20 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 18
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  115 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0980
   chunk 2 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.124724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.110277 restraints weight = 2074.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.113168 restraints weight = 1209.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.115269 restraints weight = 823.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.116691 restraints weight = 612.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.117634 restraints weight = 487.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   1546  Z= 0.099
  Angle     :  0.566   5.206   2086  Z= 0.281
  Chirality :  0.046   0.135    244
  Planarity :  0.004   0.037    263
  Dihedral  :  4.463  13.364    205
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 21.74 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.07 (0.62), residues: 200
  helix: -0.21 (0.53), residues: 109
  sheet: -1.01 (0.90), residues: 32
  loop : -1.15 (0.87), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  77 
 TYR   0.001   0.001   TYR A 107 
 PHE   0.011   0.001   PHE A  32 
 TRP   0.007   0.002   TRP A 167 
 HIS   0.001   0.000   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 1545)
  covalent geometry    : angle       0.56496 ( 2084)
  SS BOND              : bond        0.00278 (    1)
  SS BOND              : angle       1.03892 (    2)
  hydrogen bonds       : bond        0.02544 (   65)
  hydrogen bonds       : angle       4.91009 (  195)

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.058 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 22
  average time/residue: 0.0564
  time to fit residues: 1.5028
Evaluate side-chains
  21 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  115 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9980
   chunk 6 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 7 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 11 optimal weight:    0.3980
   chunk 1 optimal weight:    2.9990
   overall best weight:    2.0786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.108407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.091123 restraints weight = 2095.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.094103 restraints weight = 1274.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.096277 restraints weight = 892.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.097920 restraints weight = 680.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.099150 restraints weight = 546.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   1546  Z= 0.179
  Angle     :  0.759  16.377   2086  Z= 0.344
  Chirality :  0.049   0.141    244
  Planarity :  0.004   0.038    263
  Dihedral  :  4.776  14.818    205
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 21.74 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.24 (0.61), residues: 200
  helix: -0.41 (0.52), residues: 109
  sheet: -1.02 (0.90), residues: 32
  loop : -1.14 (0.87), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  77 
 TYR   0.005   0.001   TYR A 107 
 PHE   0.010   0.002   PHE A 168 
 TRP   0.003   0.002   TRP A 167 
 HIS   0.001   0.001   HIS A  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 1545)
  covalent geometry    : angle       0.75830 ( 2084)
  SS BOND              : bond        0.00346 (    1)
  SS BOND              : angle       1.20125 (    2)
  hydrogen bonds       : bond        0.03047 (   65)
  hydrogen bonds       : angle       5.20036 (  195)

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.038 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 20
  average time/residue: 0.0476
  time to fit residues: 1.1548
Evaluate side-chains
  24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  126 THR
Chi-restraints excluded: chain A residue  175 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 3 optimal weight:    0.2980
   chunk 4 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0270
   overall best weight:    0.5638

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.125787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.110455 restraints weight = 2052.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.113546 restraints weight = 1227.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.115727 restraints weight = 839.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.117050 restraints weight = 628.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.118261 restraints weight = 513.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   1546  Z= 0.103
  Angle     :  0.650  12.716   2086  Z= 0.301
  Chirality :  0.046   0.131    244
  Planarity :  0.004   0.036    263
  Dihedral  :  4.548  13.381    205
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 23.60 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.06 (0.62), residues: 200
  helix: -0.28 (0.52), residues: 109
  sheet: -0.89 (0.91), residues: 32
  loop : -1.05 (0.88), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A  77 
 TYR   0.001   0.001   TYR A 107 
 PHE   0.010   0.001   PHE A  32 
 TRP   0.008   0.002   TRP A 167 
 HIS   0.001   0.000   HIS A  10 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 1545)
  covalent geometry    : angle       0.64930 ( 2084)
  SS BOND              : bond        0.00290 (    1)
  SS BOND              : angle       1.04599 (    2)
  hydrogen bonds       : bond        0.02668 (   65)
  hydrogen bonds       : angle       4.94871 (  195)

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

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

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  400 Ramachandran restraints generated.
    200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.059 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 22
  average time/residue: 0.0520
  time to fit residues: 1.3728
Evaluate side-chains
  23 residues out of total 163 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 MET
Chi-restraints excluded: chain A residue  115 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 1 optimal weight:    0.3980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.125140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.110046 restraints weight = 2022.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.113038 restraints weight = 1205.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.114967 restraints weight = 832.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.116594 restraints weight = 635.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.117497 restraints weight = 507.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   1546  Z= 0.107
  Angle     :  0.632  12.077   2086  Z= 0.295
  Chirality :  0.046   0.132    244
  Planarity :  0.004   0.036    263
  Dihedral  :  4.484  13.246    205
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 23.60 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -1.04 (0.62), residues: 200
  helix: -0.22 (0.52), residues: 109
  sheet: -0.99 (0.89), residues: 32
  loop : -1.08 (0.88), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  77 
 TYR   0.001   0.001   TYR A 107 
 PHE   0.010   0.001   PHE A  32 
 TRP   0.006   0.002   TRP A 167 
 HIS   0.001   0.000   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 1545)
  covalent geometry    : angle       0.63198 ( 2084)
  SS BOND              : bond        0.00280 (    1)
  SS BOND              : angle       1.01386 (    2)
  hydrogen bonds       : bond        0.02686 (   65)
  hydrogen bonds       : angle       4.89323 (  195)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 729.66 seconds
wall clock time: 13 minutes 6.45 seconds (786.45 seconds total)