Starting phenix.real_space_refine
on Tue Feb  3 13:25:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ugy_64148/02_2026/9ugy_64148.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ugy_64148/02_2026/9ugy_64148.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ugy_64148/02_2026/9ugy_64148.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ugy_64148/02_2026/9ugy_64148.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ugy_64148/02_2026/9ugy_64148.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ugy_64148/02_2026/9ugy_64148.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.035
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       1      5.49       5
     S      20      5.16       5
     C    2089      2.51       5
     N     507      2.21       5
     O     566      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3183
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3167
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 16, 'TRANS': 398}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 16
          Unusual residues: {'GLP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.79, per 1000 atoms: 0.25
  Number of scatterers: 3183
  At special positions: 0
  Unit cell: (72.512, 70.864, 53.56, 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      20     16.00
     P       1     15.00
     O     566      8.00
     N     507      7.00
     C    2089      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: 0.18
  Conformation dependent library (CDL) restraints added in 75.0 milliseconds
  

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  748

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      86.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 27
      removed outlier: 3.618A  pdb=" N   GLY A   5 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 42
      removed outlier: 3.635A  pdb=" N   VAL A  34 " --> pdb=" O   THR A  30 " (cutoff:3.500A)
      Proline residue:  A  36  - end of helix
    Processing helix  chain 'A' and resid 45 through 74
      removed outlier: 3.545A  pdb=" N   GLY A  68 " --> pdb=" O   LYS A  64 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   VAL A  69 " --> pdb=" O   PHE A  65 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   ASP A  72 " --> pdb=" O   GLY A  68 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLN A  73 " --> pdb=" O   VAL A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 96
    Processing helix  chain 'A' and resid 99 through 129
      removed outlier: 3.706A  pdb=" N   ALA A 105 " --> pdb=" O   PRO A 101 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LEU A 106 " --> pdb=" O   VAL A 102 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   TRP A 118 " --> pdb=" O   GLN A 114 " (cutoff:3.500A)
      Proline residue:  A 119  - end of helix
    Processing helix  chain 'A' and resid 133 through 160
      removed outlier: 3.568A  pdb=" N   TRP A 137 " --> pdb=" O   GLN A 133 " (cutoff:3.500A)
      Proline residue:  A 153  - end of helix
    Processing helix  chain 'A' and resid 164 through 187
    Processing helix  chain 'A' and resid 190 through 194
    Processing helix  chain 'A' and resid 216 through 221
    Processing helix  chain 'A' and resid 225 through 254
    Processing helix  chain 'A' and resid 258 through 291
      removed outlier: 3.706A  pdb=" N   GLY A 262 " --> pdb=" O   SER A 258 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ALA A 289 " --> pdb=" O   ASP A 285 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   LYS A 290 " --> pdb=" O   ARG A 286 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ALA A 291 " --> pdb=" O   ALA A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 321
    Processing helix  chain 'A' and resid 327 through 357
      removed outlier: 4.094A  pdb=" N   ILE A 331 " --> pdb=" O   PRO A 327 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   LEU A 332 " --> pdb=" O   LYS A 328 " (cutoff:3.500A)
      Proline residue:  A 345  - end of helix
    Processing helix  chain 'A' and resid 358 through 360
      No H-bonds generated for 'chain 'A' and resid 358 through 360'
    Processing helix  chain 'A' and resid 361 through 391
      removed outlier: 3.554A  pdb=" N   LEU A 382 " --> pdb=" O   PHE A 378 " (cutoff:3.500A)
      Proline residue:  A 383  - end of helix
    Processing helix  chain 'A' and resid 392 through 414

    266 hydrogen bonds defined for protein.
    792 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: 0.30

  Time building geometry restraints manager: 0.23 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 952
        1.34 -     1.46: 701
        1.46 -     1.57: 1583
        1.57 -     1.69: 1
        1.69 -     1.81: 34
  Bond restraints: 3271
  Sorted by residual:
  bond pdb=" O6  GLP A 501 "
       pdb=" P   GLP A 501 "
    ideal  model  delta    sigma   weight residual
    1.642  1.700 -0.058 2.00e-02 2.50e+03 8.48e+00
  bond pdb=" CB  PRO A 224 "
       pdb=" CG  PRO A 224 "
    ideal  model  delta    sigma   weight residual
    1.492  1.615 -0.123 5.00e-02 4.00e+02 6.02e+00
  bond pdb=" CG  PRO A 224 "
       pdb=" CD  PRO A 224 "
    ideal  model  delta    sigma   weight residual
    1.503  1.434  0.069 3.40e-02 8.65e+02 4.13e+00
  bond pdb=" CA  VAL A 100 "
       pdb=" C   VAL A 100 "
    ideal  model  delta    sigma   weight residual
    1.520  1.530 -0.010 8.80e-03 1.29e+04 1.31e+00
  bond pdb=" C3  GLP A 501 "
       pdb=" C4  GLP A 501 "
    ideal  model  delta    sigma   weight residual
    1.505  1.484  0.021 2.00e-02 2.50e+03 1.11e+00
  ... (remaining 3266 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 4355
        2.41 -     4.83: 78
        4.83 -     7.24: 18
        7.24 -     9.65: 1
        9.65 -    12.06: 1
  Bond angle restraints: 4453
  Sorted by residual:
  angle pdb=" CA  PRO A 224 "
        pdb=" N   PRO A 224 "
        pdb=" CD  PRO A 224 "
      ideal   model   delta    sigma   weight residual
     112.00   99.94   12.06 1.40e+00 5.10e-01 7.43e+01
  angle pdb=" N   GLY A 117 "
        pdb=" CA  GLY A 117 "
        pdb=" C   GLY A 117 "
      ideal   model   delta    sigma   weight residual
     112.49  120.09   -7.60 1.21e+00 6.83e-01 3.94e+01
  angle pdb=" C   THR A  99 "
        pdb=" N   VAL A 100 "
        pdb=" CA  VAL A 100 "
      ideal   model   delta    sigma   weight residual
     120.24  124.08   -3.84 6.30e-01 2.52e+00 3.71e+01
  angle pdb=" N   PRO A 224 "
        pdb=" CD  PRO A 224 "
        pdb=" CG  PRO A 224 "
      ideal   model   delta    sigma   weight residual
     103.20   96.90    6.30 1.50e+00 4.44e-01 1.76e+01
  angle pdb=" N   VAL A 194 "
        pdb=" CA  VAL A 194 "
        pdb=" C   VAL A 194 "
      ideal   model   delta    sigma   weight residual
     112.12  108.66    3.46 8.40e-01 1.42e+00 1.70e+01
  ... (remaining 4448 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 1585
       17.64 -    35.28: 208
       35.28 -    52.92: 68
       52.92 -    70.56: 11
       70.56 -    88.20: 2
  Dihedral angle restraints: 1874
    sinusoidal: 697
      harmonic: 1177
  Sorted by residual:
  dihedral pdb=" CA  PRO A 224 "
           pdb=" C   PRO A 224 "
           pdb=" N   TYR A 225 "
           pdb=" CA  TYR A 225 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.84   16.16     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CA  ASP A 325 "
           pdb=" CB  ASP A 325 "
           pdb=" CG  ASP A 325 "
           pdb=" OD1 ASP A 325 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.29   55.29     1      2.00e+01 2.50e-03 1.03e+01
  dihedral pdb=" CB  GLU A 270 "
           pdb=" CG  GLU A 270 "
           pdb=" CD  GLU A 270 "
           pdb=" OE1 GLU A 270 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.20  -88.20     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 1871 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 331
       0.032 -    0.065: 126
       0.065 -    0.097: 38
       0.097 -    0.129: 9
       0.129 -    0.162: 1
  Chirality restraints: 505
  Sorted by residual:
  chirality pdb=" CB  VAL A 102 "
            pdb=" CA  VAL A 102 "
            pdb=" CG1 VAL A 102 "
            pdb=" CG2 VAL A 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.54e-01
  chirality pdb=" CA  PRO A 345 "
            pdb=" N   PRO A 345 "
            pdb=" C   PRO A 345 "
            pdb=" CB  PRO A 345 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.64e-01
  chirality pdb=" CA  VAL A 102 "
            pdb=" N   VAL A 102 "
            pdb=" C   VAL A 102 "
            pdb=" CB  VAL A 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 2.79e-01
  ... (remaining 502 not shown)

  Planarity restraints: 544
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 223 "    0.113 5.00e-02 4.00e+02   1.62e-01 4.18e+01
        pdb=" N   PRO A 224 "   -0.279 5.00e-02 4.00e+02
        pdb=" CA  PRO A 224 "    0.085 5.00e-02 4.00e+02
        pdb=" CD  PRO A 224 "    0.081 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 344 "   -0.055 5.00e-02 4.00e+02   8.34e-02 1.11e+01
        pdb=" N   PRO A 345 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO A 345 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 345 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A  42 "   -0.045 5.00e-02 4.00e+02   6.87e-02 7.55e+00
        pdb=" N   PRO A  43 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 541 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 112
        2.71 -     3.26: 3366
        3.26 -     3.81: 5630
        3.81 -     4.35: 6394
        4.35 -     4.90: 10856
  Nonbonded interactions: 26358
  Sorted by model distance:
  nonbonded pdb=" O   GLY A  50 "
            pdb=" OG  SER A  54 "
     model   vdw
     2.167 3.040
  nonbonded pdb=" O   PHE A  93 "
            pdb=" OG  SER A  97 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   LEU A 317 "
            pdb=" OG1 THR A 321 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   PHE A  26 "
            pdb=" OG1 THR A  30 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OD1 ASN A  27 "
            pdb=" OG  SER A 172 "
     model   vdw
     2.238 3.040
  ... (remaining 26353 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:             0.790
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.880
  Find NCS groups from input model:        0.010
  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:0.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
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   0.123   3271  Z= 0.186
  Angle     :  0.856  12.065   4453  Z= 0.533
  Chirality :  0.038   0.162    505
  Planarity :  0.010   0.162    544
  Dihedral  : 17.695  88.202   1126
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  5.60 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 33.23 %
    Favored  : 66.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.43), residues: 411
  helix:  1.87 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.70 (0.74), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 197 
 TYR   0.009   0.001   TYR A   8 
 PHE   0.022   0.002   PHE A  18 
 TRP   0.009   0.001   TRP A 137 
 HIS   0.002   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 3271)
  covalent geometry    : angle       0.85645 ( 4453)
  hydrogen bonds       : bond        0.11132 (  266)
  hydrogen bonds       : angle       5.33808 (  792)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.7950 (m-40)
  outliers start: 1
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0890
  time to fit residues: 4.7239
Evaluate side-chains
  43 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.4980
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.3980
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 301 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.207794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.169097 restraints weight = 3661.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.173347 restraints weight = 2302.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.175724 restraints weight = 1742.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.177491 restraints weight = 1484.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.178270 restraints weight = 1352.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.1006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3271  Z= 0.165
  Angle     :  0.681   7.233   4453  Z= 0.350
  Chirality :  0.041   0.273    505
  Planarity :  0.007   0.098    544
  Dihedral  :  5.015  52.106    466
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  5.60 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 28.14 %
    Favored  : 67.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.43), residues: 411
  helix:  1.97 (0.28), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.46 (0.74), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 418 
 TYR   0.013   0.001   TYR A  21 
 PHE   0.015   0.002   PHE A 338 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 3271)
  covalent geometry    : angle       0.68071 ( 4453)
  hydrogen bonds       : bond        0.05111 (  266)
  hydrogen bonds       : angle       4.50120 (  792)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: A  250 PHE cc_start: 0.8427 (t80) cc_final: 0.8003 (t80)
REVERT: A  401 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7152 (tm-30)
  outliers start: 14
  outliers final: 4
  residues processed: 54
  average time/residue: 0.0858
  time to fit residues: 5.5201
Evaluate side-chains
  47 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  266 MET
Chi-restraints excluded: chain A residue  401 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 19 optimal weight:    0.1980
   chunk 22 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 189 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.205884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.166987 restraints weight = 3671.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.171131 restraints weight = 2309.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.173232 restraints weight = 1762.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.175226 restraints weight = 1519.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.176018 restraints weight = 1375.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.1448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3271  Z= 0.165
  Angle     :  0.703  14.513   4453  Z= 0.348
  Chirality :  0.042   0.299    505
  Planarity :  0.007   0.071    544
  Dihedral  :  4.361  19.651    464
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  5.11 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 27.84 %
    Favored  : 67.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.05 (0.42), residues: 411
  helix:  2.00 (0.28), residues: 335
  sheet:  None (None), residues: 0
  loop : -1.63 (0.73), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  10 
 TYR   0.015   0.001   TYR A  21 
 PHE   0.013   0.002   PHE A 338 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 3271)
  covalent geometry    : angle       0.70305 ( 4453)
  hydrogen bonds       : bond        0.05054 (  266)
  hydrogen bonds       : angle       4.36790 (  792)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.067 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6822 (mp)
REVERT: A  250 PHE cc_start: 0.8364 (t80) cc_final: 0.7968 (t80)
REVERT: A  401 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7178 (tm-30)
  outliers start: 14
  outliers final: 6
  residues processed: 57
  average time/residue: 0.0615
  time to fit residues: 4.1681
Evaluate side-chains
  50 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  401 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0970
   chunk 32 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 24 optimal weight:    6.9990
   chunk 20 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.4242 r_free = 0.4242 target = 0.206349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.167223 restraints weight = 3637.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.171189 restraints weight = 2296.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.173798 restraints weight = 1742.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.175067 restraints weight = 1493.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.175415 restraints weight = 1367.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3271  Z= 0.156
  Angle     :  0.669   9.640   4453  Z= 0.337
  Chirality :  0.041   0.286    505
  Planarity :  0.006   0.066    544
  Dihedral  :  4.372  19.193    464
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  5.11 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 28.44 %
    Favored  : 66.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.21 (0.43), residues: 411
  helix:  2.09 (0.28), residues: 335
  sheet:  None (None), residues: 0
  loop : -1.46 (0.74), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 418 
 TYR   0.021   0.002   TYR A 316 
 PHE   0.013   0.001   PHE A 338 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 3271)
  covalent geometry    : angle       0.66921 ( 4453)
  hydrogen bonds       : bond        0.04943 (  266)
  hydrogen bonds       : angle       4.32633 (  792)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 40
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A  141 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6756 (mp)
REVERT: A  250 PHE cc_start: 0.8297 (t80) cc_final: 0.8016 (t80)
REVERT: A  401 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7153 (tm-30)
  outliers start: 16
  outliers final: 9
  residues processed: 53
  average time/residue: 0.0720
  time to fit residues: 4.6656
Evaluate side-chains
  48 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 37
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  248 GLN
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  401 GLU
Chi-restraints excluded: chain A residue  417 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    0.0270
   chunk 30 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
A 189 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.205672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.166347 restraints weight = 3650.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.170415 restraints weight = 2302.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.172901 restraints weight = 1760.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.174162 restraints weight = 1511.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.174215 restraints weight = 1382.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3271  Z= 0.162
  Angle     :  0.662   8.444   4453  Z= 0.335
  Chirality :  0.041   0.279    505
  Planarity :  0.006   0.065    544
  Dihedral  :  4.357  19.165    464
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  5.35 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 29.34 %
    Favored  : 66.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.27 (0.43), residues: 411
  helix:  2.14 (0.28), residues: 334
  sheet:  None (None), residues: 0
  loop : -1.46 (0.74), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 418 
 TYR   0.019   0.002   TYR A  21 
 PHE   0.012   0.001   PHE A 338 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 3271)
  covalent geometry    : angle       0.66157 ( 4453)
  hydrogen bonds       : bond        0.05001 (  266)
  hydrogen bonds       : angle       4.33649 (  792)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 38
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6798 (mp)
REVERT: A  250 PHE cc_start: 0.8242 (t80) cc_final: 0.7975 (t80)
  outliers start: 15
  outliers final: 9
  residues processed: 51
  average time/residue: 0.0688
  time to fit residues: 4.3593
Evaluate side-chains
  48 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 38
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  243 CYS
Chi-restraints excluded: chain A residue  248 GLN
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  304 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0270
   chunk 35 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
A 189 ASN
A 248 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.206248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.166950 restraints weight = 3622.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.170927 restraints weight = 2286.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.173578 restraints weight = 1756.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.174514 restraints weight = 1503.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.174519 restraints weight = 1398.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3271  Z= 0.155
  Angle     :  0.644   8.323   4453  Z= 0.329
  Chirality :  0.041   0.270    505
  Planarity :  0.006   0.064    544
  Dihedral  :  4.363  18.556    464
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.11 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 28.74 %
    Favored  : 65.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.32 (0.43), residues: 411
  helix:  2.16 (0.29), residues: 334
  sheet:  None (None), residues: 0
  loop : -1.35 (0.74), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 418 
 TYR   0.019   0.002   TYR A  21 
 PHE   0.012   0.001   PHE A 338 
 TRP   0.008   0.001   TRP A 246 
 HIS   0.001   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3271)
  covalent geometry    : angle       0.64425 ( 4453)
  hydrogen bonds       : bond        0.04920 (  266)
  hydrogen bonds       : angle       4.30131 (  792)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 36
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6813 (mp)
REVERT: A  305 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8281 (mm)
  outliers start: 20
  outliers final: 14
  residues processed: 53
  average time/residue: 0.0579
  time to fit residues: 3.8295
Evaluate side-chains
  53 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 37
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  243 CYS
Chi-restraints excluded: chain A residue  248 GLN
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  417 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 189 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.205458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.166506 restraints weight = 3715.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.170680 restraints weight = 2331.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.173198 restraints weight = 1769.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.174887 restraints weight = 1501.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.175603 restraints weight = 1359.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3271  Z= 0.164
  Angle     :  0.659   8.391   4453  Z= 0.339
  Chirality :  0.041   0.261    505
  Planarity :  0.006   0.064    544
  Dihedral  :  4.368  18.308    464
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.35 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  6.59 %
    Allowed  : 28.14 %
    Favored  : 65.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.42 (0.43), residues: 411
  helix:  2.20 (0.29), residues: 334
  sheet:  None (None), residues: 0
  loop : -1.12 (0.76), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A  77 
 TYR   0.020   0.002   TYR A  21 
 PHE   0.013   0.002   PHE A 250 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 3271)
  covalent geometry    : angle       0.65901 ( 4453)
  hydrogen bonds       : bond        0.04917 (  266)
  hydrogen bonds       : angle       4.30530 (  792)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 36
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6796 (mp)
REVERT: A  145 MET cc_start: 0.6646 (ttm) cc_final: 0.6441 (ttp)
REVERT: A  250 PHE cc_start: 0.8334 (t80) cc_final: 0.8036 (t80)
REVERT: A  266 MET cc_start: 0.7127 (ttp) cc_final: 0.6860 (ttt)
REVERT: A  305 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8302 (mm)
  outliers start: 22
  outliers final: 13
  residues processed: 55
  average time/residue: 0.0637
  time to fit residues: 4.3462
Evaluate side-chains
  51 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 36
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  243 CYS
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  329 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0010
   chunk 5 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 189 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.205005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.165829 restraints weight = 3764.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.170023 restraints weight = 2362.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.172239 restraints weight = 1794.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.174274 restraints weight = 1529.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.174618 restraints weight = 1382.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3271  Z= 0.164
  Angle     :  0.664   8.548   4453  Z= 0.343
  Chirality :  0.041   0.258    505
  Planarity :  0.006   0.063    544
  Dihedral  :  4.399  18.174    464
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  4.87 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 29.34 %
    Favored  : 65.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.52 (0.43), residues: 411
  helix:  2.26 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -0.99 (0.75), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 197 
 TYR   0.020   0.002   TYR A  21 
 PHE   0.012   0.001   PHE A 338 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 3271)
  covalent geometry    : angle       0.66400 ( 4453)
  hydrogen bonds       : bond        0.04931 (  266)
  hydrogen bonds       : angle       4.30446 (  792)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 37
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6813 (mp)
REVERT: A  300 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7445 (mtt180)
REVERT: A  305 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8293 (mm)
  outliers start: 18
  outliers final: 15
  residues processed: 53
  average time/residue: 0.0716
  time to fit residues: 4.6776
Evaluate side-chains
  55 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 37
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  243 CYS
Chi-restraints excluded: chain A residue  248 GLN
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  417 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 19 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 189 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.205652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.166253 restraints weight = 3707.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.170413 restraints weight = 2368.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.172620 restraints weight = 1805.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.174465 restraints weight = 1548.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.175267 restraints weight = 1404.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3271  Z= 0.164
  Angle     :  0.666   8.336   4453  Z= 0.344
  Chirality :  0.041   0.253    505
  Planarity :  0.006   0.063    544
  Dihedral  :  4.427  20.111    464
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  4.87 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 29.04 %
    Favored  : 64.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.57 (0.43), residues: 411
  helix:  2.26 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -0.80 (0.79), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 197 
 TYR   0.016   0.002   TYR A  21 
 PHE   0.018   0.002   PHE A  18 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 3271)
  covalent geometry    : angle       0.66633 ( 4453)
  hydrogen bonds       : bond        0.04936 (  266)
  hydrogen bonds       : angle       4.32240 (  792)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 38
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  141 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6809 (mp)
REVERT: A  300 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7451 (mtt180)
REVERT: A  305 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8294 (mm)
  outliers start: 20
  outliers final: 14
  residues processed: 56
  average time/residue: 0.0711
  time to fit residues: 4.8592
Evaluate side-chains
  55 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 38
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  243 CYS
Chi-restraints excluded: chain A residue  248 GLN
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  304 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  411 PHE
Chi-restraints excluded: chain A residue  417 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0770
   chunk 19 optimal weight:    0.0000
   chunk 37 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.4342

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

Flipped N/Q/H residues before XYZ refinement:
A 189 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.207588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.169108 restraints weight = 3650.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.172980 restraints weight = 2318.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.175227 restraints weight = 1771.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.177176 restraints weight = 1512.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.177633 restraints weight = 1364.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.2192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3271  Z= 0.148
  Angle     :  0.647   8.086   4453  Z= 0.333
  Chirality :  0.040   0.243    505
  Planarity :  0.006   0.064    544
  Dihedral  :  4.392  20.414    464
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.11 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 29.64 %
    Favored  : 64.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.67 (0.43), residues: 411
  helix:  2.31 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -0.71 (0.78), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  10 
 TYR   0.014   0.001   TYR A  21 
 PHE   0.016   0.002   PHE A  18 
 TRP   0.008   0.001   TRP A 246 
 HIS   0.001   0.000   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 3271)
  covalent geometry    : angle       0.64747 ( 4453)
  hydrogen bonds       : bond        0.04780 (  266)
  hydrogen bonds       : angle       4.32034 (  792)

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

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

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  822 Ramachandran restraints generated.
    411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 36
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  141 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6787 (mp)
REVERT: A  300 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7434 (mtt180)
REVERT: A  305 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8232 (mm)
  outliers start: 20
  outliers final: 14
  residues processed: 53
  average time/residue: 0.0530
  time to fit residues: 3.5798
Evaluate side-chains
  52 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 35
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 SER
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  138 TRP
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  216 THR
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  243 CYS
Chi-restraints excluded: chain A residue  248 GLN
Chi-restraints excluded: chain A residue  300 ARG
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  411 PHE
Chi-restraints excluded: chain A residue  417 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 189 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.204045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.164162 restraints weight = 3700.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.168176 restraints weight = 2376.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.170770 restraints weight = 1828.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.171913 restraints weight = 1560.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.171913 restraints weight = 1438.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3271  Z= 0.185
  Angle     :  0.691   9.551   4453  Z= 0.353
  Chirality :  0.042   0.250    505
  Planarity :  0.006   0.065    544
  Dihedral  :  4.444  20.484    464
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.35 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 30.24 %
    Favored  : 64.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.51 (0.43), residues: 411
  helix:  2.19 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -0.70 (0.77), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 300 
 TYR   0.020   0.002   TYR A  21 
 PHE   0.017   0.002   PHE A  18 
 TRP   0.012   0.001   TRP A 107 
 HIS   0.001   0.001   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 3271)
  covalent geometry    : angle       0.69050 ( 4453)
  hydrogen bonds       : bond        0.05194 (  266)
  hydrogen bonds       : angle       4.40315 (  792)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 717.93 seconds
wall clock time: 13 minutes 1.97 seconds (781.97 seconds total)