Starting phenix.real_space_refine
on Tue Feb  3 13:24:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9x95_66660/02_2026/9x95_66660_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9x95_66660/02_2026/9x95_66660.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9x95_66660/02_2026/9x95_66660_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9x95_66660/02_2026/9x95_66660_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9x95_66660/02_2026/9x95_66660.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9x95_66660/02_2026/9x95_66660.map"
  }
  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: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    2083      2.51       5
     N     506      2.21       5
     O     558      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 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: 3167
  Number of models: 1
  Model: ""
    Number of chains: 1
    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
  Time building chain proxies: 1.05, per 1000 atoms: 0.33
  Number of scatterers: 3167
  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: 4
    Type Number    sf(0)
     S      20     16.00
     O     558      8.00
     N     506      7.00
     C    2083      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.31
  Conformation dependent library (CDL) restraints added in 134.3 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
      87.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  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: 4.027A  pdb=" N   ALA A  59 " --> pdb=" O   SER A  55 " (cutoff:3.500A)
      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
      removed outlier: 3.502A  pdb=" N   TRP A  96 " --> pdb=" O   ILE A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 129
      removed outlier: 3.819A  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 223 through 254
      removed outlier: 4.072A  pdb=" N   TRP A 227 " --> pdb=" O   SER A 223 " (cutoff:3.500A)
    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

    267 hydrogen bonds defined for protein.
    795 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: 0.48

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 945
        1.34 -     1.46: 573
        1.46 -     1.57: 1704
        1.57 -     1.69: 0
        1.69 -     1.81: 33
  Bond restraints: 3255
  Sorted by residual:
  bond pdb=" N   TRP A 118 "
       pdb=" CA  TRP A 118 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.04e-02 9.25e+03 1.07e+01
  bond pdb=" N   VAL A 102 "
       pdb=" CA  VAL A 102 "
    ideal  model  delta    sigma   weight residual
    1.461  1.498 -0.037 1.19e-02 7.06e+03 9.71e+00
  bond pdb=" N   ASP A  45 "
       pdb=" CA  ASP A  45 "
    ideal  model  delta    sigma   weight residual
    1.454  1.491 -0.037 1.23e-02 6.61e+03 9.26e+00
  bond pdb=" CA  SER A  55 "
       pdb=" CB  SER A  55 "
    ideal  model  delta    sigma   weight residual
    1.530  1.481  0.049 1.69e-02 3.50e+03 8.46e+00
  bond pdb=" N   VAL A 228 "
       pdb=" CA  VAL A 228 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 8.11e+00
  ... (remaining 3250 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 3990
        1.44 -     2.87: 338
        2.87 -     4.31: 74
        4.31 -     5.75: 22
        5.75 -     7.19: 5
  Bond angle restraints: 4429
  Sorted by residual:
  angle pdb=" C   SER A 223 "
        pdb=" N   PRO A 224 "
        pdb=" CA  PRO A 224 "
      ideal   model   delta    sigma   weight residual
     119.05  123.74   -4.69 1.11e+00 8.12e-01 1.79e+01
  angle pdb=" N   GLY A 117 "
        pdb=" CA  GLY A 117 "
        pdb=" C   GLY A 117 "
      ideal   model   delta    sigma   weight residual
     112.73  117.73   -5.00 1.20e+00 6.94e-01 1.73e+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
  angle pdb=" C   VAL A 100 "
        pdb=" CA  VAL A 100 "
        pdb=" CB  VAL A 100 "
      ideal   model   delta    sigma   weight residual
     114.35  109.99    4.36 1.06e+00 8.90e-01 1.69e+01
  angle pdb=" N   VAL A 100 "
        pdb=" CA  VAL A 100 "
        pdb=" CB  VAL A 100 "
      ideal   model   delta    sigma   weight residual
     110.50  113.01   -2.51 6.30e-01 2.52e+00 1.59e+01
  ... (remaining 4424 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 1566
       17.64 -    35.28: 195
       35.28 -    52.92: 77
       52.92 -    70.56: 11
       70.56 -    88.20: 2
  Dihedral angle restraints: 1851
    sinusoidal: 674
      harmonic: 1177
  Sorted by residual:
  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
  dihedral pdb=" CG  ARG A 418 "
           pdb=" CD  ARG A 418 "
           pdb=" NE  ARG A 418 "
           pdb=" CZ  ARG A 418 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.59   43.41     2      1.50e+01 4.44e-03 1.01e+01
  ... (remaining 1848 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 356
       0.043 -    0.087: 114
       0.087 -    0.130: 24
       0.130 -    0.173: 5
       0.173 -    0.217: 1
  Chirality restraints: 500
  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   -2.41   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  CYS A 121 "
            pdb=" N   CYS A 121 "
            pdb=" C   CYS A 121 "
            pdb=" CB  CYS A 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.61e-01
  chirality pdb=" CA  LEU A 221 "
            pdb=" N   LEU A 221 "
            pdb=" C   LEU A 221 "
            pdb=" CB  LEU A 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.49e-01
  ... (remaining 497 not shown)

  Planarity restraints: 544
  Sorted by residual:
                                 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
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 152 "    0.035 5.00e-02 4.00e+02   5.41e-02 4.67e+00
        pdb=" N   PRO A 153 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 153 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 153 "    0.030 5.00e-02 4.00e+02
  ... (remaining 541 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 570
        2.76 -     3.30: 3206
        3.30 -     3.83: 5764
        3.83 -     4.37: 6142
        4.37 -     4.90: 10643
  Nonbonded interactions: 26325
  Sorted by model distance:
  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
  nonbonded pdb=" O   SER A  75 "
            pdb=" NZ  LYS A 123 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" OG  SER A 356 "
            pdb=" O   THR A 419 "
     model   vdw
     2.283 3.040
  ... (remaining 26320 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:             0.970
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.720
  Find NCS groups from input model:        0.020
  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:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
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   0.051   3255  Z= 0.349
  Angle     :  0.938   7.186   4429  Z= 0.647
  Chirality :  0.044   0.217    500
  Planarity :  0.007   0.083    544
  Dihedral  : 18.092  88.202   1103
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 14.98
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  4.87 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 32.34 %
    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:  2.08 (0.43), residues: 411
  helix:  2.07 (0.29), residues: 329
  sheet:  None (None), residues: 0
  loop : -1.58 (0.73), residues: 82

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   0.002   TRP A 137 
 HIS   0.002   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 ( 3255)
  covalent geometry    : angle       0.93817 ( 4429)
  hydrogen bonds       : bond        0.13300 (  267)
  hydrogen bonds       : angle       5.63339 (  795)

*********************** 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
  52 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.067 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.7975 (m-40)
REVERT: A  229 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.6965 (tt)
  outliers start: 8
  outliers final: 1
  residues processed: 51
  average time/residue: 0.0650
  time to fit residues: 3.9384
Evaluate side-chains
  44 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue  189 ASN
Chi-restraints excluded: chain A residue  229 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4204 r_free = 0.4204 target = 0.202911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.162309 restraints weight = 3744.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.166510 restraints weight = 2216.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.169025 restraints weight = 1662.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.170881 restraints weight = 1414.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.171531 restraints weight = 1279.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.1094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3255  Z= 0.175
  Angle     :  0.669   7.335   4429  Z= 0.352
  Chirality :  0.040   0.126    500
  Planarity :  0.006   0.072    544
  Dihedral  :  5.435  52.024    447
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  4.87 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 30.54 %
    Favored  : 65.87 %
  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:  2.09 (0.42), residues: 411
  helix:  1.98 (0.28), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.25 (0.76), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  10 
 TYR   0.015   0.002   TYR A  21 
 PHE   0.014   0.002   PHE A 338 
 TRP   0.008   0.001   TRP A 246 
 HIS   0.001   0.000   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 3255)
  covalent geometry    : angle       0.66926 ( 4429)
  hydrogen bonds       : bond        0.05287 (  267)
  hydrogen bonds       : angle       4.53870 (  795)

*********************** 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
  55 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7366 (tt)
REVERT: A  250 PHE cc_start: 0.8440 (t80) cc_final: 0.8109 (t80)
REVERT: A  401 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7197 (tm-30)
  outliers start: 12
  outliers final: 1
  residues processed: 52
  average time/residue: 0.0792
  time to fit residues: 4.9101
Evaluate side-chains
  43 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue  229 LEU
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 25 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0870
   chunk 9 optimal weight:    0.9980
   chunk 4 optimal weight:    0.3980
   chunk 2 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 7 optimal weight:    0.3980
   chunk 33 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.5158

-------------------------------------------------------------------------------
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 = 0.204329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.163888 restraints weight = 3707.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.168172 restraints weight = 2198.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.170768 restraints weight = 1647.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.171635 restraints weight = 1416.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.173012 restraints weight = 1315.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.1406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3255  Z= 0.150
  Angle     :  0.677  14.236   4429  Z= 0.338
  Chirality :  0.039   0.139    500
  Planarity :  0.006   0.068    544
  Dihedral  :  4.633  33.005    443
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  4.87 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 29.34 %
    Favored  : 65.57 %
  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:  2.14 (0.42), residues: 411
  helix:  2.08 (0.28), residues: 331
  sheet:  None (None), residues: 0
  loop : -1.48 (0.73), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  10 
 TYR   0.015   0.001   TYR A  21 
 PHE   0.014   0.001   PHE A 338 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3255)
  covalent geometry    : angle       0.67741 ( 4429)
  hydrogen bonds       : bond        0.04933 (  267)
  hydrogen bonds       : angle       4.34416 (  795)

*********************** 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: 17
    poor density    : 42
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
REVERT: A  250 PHE cc_start: 0.8343 (t80) cc_final: 0.7969 (t80)
REVERT: A  401 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7192 (tm-30)
REVERT: A  418 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6659 (ttm170)
  outliers start: 17
  outliers final: 5
  residues processed: 56
  average time/residue: 0.0715
  time to fit residues: 4.8688
Evaluate side-chains
  49 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 TRP
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
Chi-restraints excluded: chain A residue  418 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.2980
   chunk 9 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0970
   chunk 19 optimal weight:    8.9990
   chunk 37 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.4378

-------------------------------------------------------------------------------
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 = 0.4218 r_free = 0.4218 target = 0.204758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.169772 restraints weight = 3696.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.168348 restraints weight = 2662.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.169235 restraints weight = 2382.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.169627 restraints weight = 2188.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.170325 restraints weight = 1935.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3255  Z= 0.143
  Angle     :  0.637   9.207   4429  Z= 0.323
  Chirality :  0.038   0.136    500
  Planarity :  0.005   0.065    544
  Dihedral  :  4.226  16.332    441
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  4.38 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 29.34 %
    Favored  : 65.87 %
  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:  2.28 (0.42), residues: 411
  helix:  2.17 (0.28), residues: 331
  sheet:  None (None), residues: 0
  loop : -1.39 (0.73), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  77 
 TYR   0.016   0.001   TYR A  21 
 PHE   0.013   0.001   PHE A 338 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.001   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 3255)
  covalent geometry    : angle       0.63672 ( 4429)
  hydrogen bonds       : bond        0.04753 (  267)
  hydrogen bonds       : angle       4.29325 (  795)

*********************** 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
  61 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 45
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6929 (mp)
REVERT: A  401 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7168 (tm-30)
REVERT: A  418 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6820 (ttm170)
  outliers start: 16
  outliers final: 7
  residues processed: 58
  average time/residue: 0.0643
  time to fit residues: 4.5651
Evaluate side-chains
  54 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 SER
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  216 THR
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  418 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4191 r_free = 0.4191 target = 0.202230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.163272 restraints weight = 3675.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.166991 restraints weight = 2326.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.169469 restraints weight = 1801.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.170442 restraints weight = 1541.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.171523 restraints weight = 1424.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3255  Z= 0.164
  Angle     :  0.633   8.476   4429  Z= 0.325
  Chirality :  0.038   0.140    500
  Planarity :  0.005   0.065    544
  Dihedral  :  4.210  16.100    441
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  4.62 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 28.14 %
    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:  2.32 (0.42), residues: 411
  helix:  2.19 (0.28), residues: 331
  sheet:  None (None), residues: 0
  loop : -1.34 (0.73), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 300 
 TYR   0.016   0.001   TYR A  21 
 PHE   0.012   0.002   PHE A 338 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 3255)
  covalent geometry    : angle       0.63284 ( 4429)
  hydrogen bonds       : bond        0.04870 (  267)
  hydrogen bonds       : angle       4.27391 (  795)

*********************** 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
  61 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 42
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A  141 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6868 (mp)
REVERT: A  250 PHE cc_start: 0.8388 (t80) cc_final: 0.8180 (t80)
REVERT: A  415 ARG cc_start: 0.5835 (ptm160) cc_final: 0.5610 (ptt90)
REVERT: A  418 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6790 (ttm170)
  outliers start: 19
  outliers final: 10
  residues processed: 57
  average time/residue: 0.0737
  time to fit residues: 5.1230
Evaluate side-chains
  55 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 SER
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  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  417 ILE
Chi-restraints excluded: chain A residue  418 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0030
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.5190

-------------------------------------------------------------------------------
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 = 0.4205 r_free = 0.4205 target = 0.203903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.163811 restraints weight = 3697.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.168102 restraints weight = 2180.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.170740 restraints weight = 1625.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.172309 restraints weight = 1377.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.172309 restraints weight = 1248.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3255  Z= 0.144
  Angle     :  0.622   8.216   4429  Z= 0.319
  Chirality :  0.038   0.148    500
  Planarity :  0.005   0.063    544
  Dihedral  :  4.204  16.067    441
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  4.38 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  : 28.44 %
    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:  2.43 (0.42), residues: 411
  helix:  2.25 (0.28), residues: 331
  sheet:  None (None), residues: 0
  loop : -1.23 (0.73), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  10 
 TYR   0.016   0.001   TYR A  21 
 PHE   0.012   0.001   PHE A 338 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3255)
  covalent geometry    : angle       0.62181 ( 4429)
  hydrogen bonds       : bond        0.04690 (  267)
  hydrogen bonds       : angle       4.20253 (  795)

*********************** 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
  64 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 43
  time to evaluate  : 0.069 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6829 (mp)
REVERT: A  250 PHE cc_start: 0.8267 (t80) cc_final: 0.7914 (t80)
REVERT: A  305 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8256 (mm)
REVERT: A  415 ARG cc_start: 0.5833 (ptm160) cc_final: 0.5618 (ptt90)
REVERT: A  418 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6749 (ttm170)
  outliers start: 21
  outliers final: 11
  residues processed: 61
  average time/residue: 0.0466
  time to fit residues: 3.5198
Evaluate side-chains
  53 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 SER
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  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
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  418 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 20 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 = 0.4180 r_free = 0.4180 target = 0.201580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.161672 restraints weight = 3772.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.165960 restraints weight = 2222.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.168698 restraints weight = 1647.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.169970 restraints weight = 1399.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.169970 restraints weight = 1281.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3255  Z= 0.172
  Angle     :  0.637   8.533   4429  Z= 0.329
  Chirality :  0.039   0.153    500
  Planarity :  0.005   0.063    544
  Dihedral  :  4.263  17.585    441
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  4.87 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  6.89 %
    Allowed  : 28.14 %
    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:  2.35 (0.43), residues: 411
  helix:  2.18 (0.28), residues: 331
  sheet:  None (None), residues: 0
  loop : -1.20 (0.73), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 300 
 TYR   0.018   0.002   TYR A  21 
 PHE   0.011   0.001   PHE A 338 
 TRP   0.011   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 3255)
  covalent geometry    : angle       0.63680 ( 4429)
  hydrogen bonds       : bond        0.04912 (  267)
  hydrogen bonds       : angle       4.24931 (  795)

*********************** 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
  63 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 40
  time to evaluate  : 0.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  141 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6898 (mp)
REVERT: A  250 PHE cc_start: 0.8177 (t80) cc_final: 0.7926 (t80)
REVERT: A  266 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6870 (ttt)
REVERT: A  305 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8296 (mm)
REVERT: A  415 ARG cc_start: 0.5867 (ptm160) cc_final: 0.5662 (ptt90)
REVERT: A  418 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6743 (ttm170)
  outliers start: 23
  outliers final: 11
  residues processed: 57
  average time/residue: 0.0469
  time to fit residues: 3.2648
Evaluate side-chains
  55 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 40
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 SER
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  216 THR
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  243 CYS
Chi-restraints excluded: chain A residue  266 MET
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
Chi-restraints excluded: chain A residue  418 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 28 optimal weight:    0.3980
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   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 189 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.202781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.162766 restraints weight = 3828.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.167127 restraints weight = 2226.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.169863 restraints weight = 1638.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.171211 restraints weight = 1381.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.172260 restraints weight = 1258.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3255  Z= 0.152
  Angle     :  0.620   8.292   4429  Z= 0.321
  Chirality :  0.039   0.159    500
  Planarity :  0.005   0.063    544
  Dihedral  :  4.248  15.955    441
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  4.38 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 29.94 %
    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:  2.44 (0.43), residues: 411
  helix:  2.24 (0.28), residues: 331
  sheet:  None (None), residues: 0
  loop : -1.11 (0.75), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 197 
 TYR   0.018   0.001   TYR A  21 
 PHE   0.015   0.001   PHE A  18 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3255)
  covalent geometry    : angle       0.61979 ( 4429)
  hydrogen bonds       : bond        0.04753 (  267)
  hydrogen bonds       : angle       4.22879 (  795)

*********************** 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
  58 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 39
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.8477 (ttm) cc_final: 0.8190 (ttm)
REVERT: A  141 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6842 (mp)
REVERT: A  305 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8296 (mm)
REVERT: A  415 ARG cc_start: 0.5825 (ptm160) cc_final: 0.5617 (ptt90)
REVERT: A  418 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6655 (ttm170)
  outliers start: 19
  outliers final: 12
  residues processed: 56
  average time/residue: 0.0630
  time to fit residues: 4.3226
Evaluate side-chains
  54 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 39
  time to evaluate  : 0.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 SER
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  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
Chi-restraints excluded: chain A residue  418 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 4 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0030
   chunk 40 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.5390

-------------------------------------------------------------------------------
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 = 0.4196 r_free = 0.4196 target = 0.203304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.163631 restraints weight = 3728.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.167981 restraints weight = 2195.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.170494 restraints weight = 1630.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.172188 restraints weight = 1378.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.172205 restraints weight = 1255.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3255  Z= 0.148
  Angle     :  0.619   8.292   4429  Z= 0.323
  Chirality :  0.039   0.153    500
  Planarity :  0.005   0.063    544
  Dihedral  :  4.224  17.487    441
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  4.62 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 30.24 %
    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:  2.51 (0.43), residues: 411
  helix:  2.28 (0.28), residues: 331
  sheet:  None (None), residues: 0
  loop : -1.03 (0.75), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  10 
 TYR   0.015   0.001   TYR A  21 
 PHE   0.016   0.002   PHE A  18 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3255)
  covalent geometry    : angle       0.61912 ( 4429)
  hydrogen bonds       : bond        0.04713 (  267)
  hydrogen bonds       : angle       4.20596 (  795)

*********************** 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
  57 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 39
  time to evaluate  : 0.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.8472 (ttm) cc_final: 0.8221 (ttm)
REVERT: A  141 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6809 (mp)
REVERT: A  250 PHE cc_start: 0.8230 (t80) cc_final: 0.7831 (t80)
REVERT: A  305 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8276 (mm)
REVERT: A  415 ARG cc_start: 0.5836 (ptm160) cc_final: 0.5596 (ptt90)
REVERT: A  418 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6746 (ttm170)
  outliers start: 18
  outliers final: 12
  residues processed: 54
  average time/residue: 0.0479
  time to fit residues: 3.1921
Evaluate side-chains
  55 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 40
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 SER
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  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
Chi-restraints excluded: chain A residue  418 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0060
   chunk 11 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   overall best weight:    0.5396

-------------------------------------------------------------------------------
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 = 0.4200 r_free = 0.4200 target = 0.203638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.164125 restraints weight = 3760.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.168360 restraints weight = 2215.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.171070 restraints weight = 1644.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.172370 restraints weight = 1389.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.172969 restraints weight = 1266.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3255  Z= 0.147
  Angle     :  0.619   8.354   4429  Z= 0.323
  Chirality :  0.039   0.154    500
  Planarity :  0.005   0.063    544
  Dihedral  :  4.210  16.723    441
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  4.38 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 29.94 %
    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:  2.52 (0.43), residues: 411
  helix:  2.26 (0.28), residues: 331
  sheet:  None (None), residues: 0
  loop : -0.95 (0.75), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  10 
 TYR   0.015   0.001   TYR A  21 
 PHE   0.014   0.001   PHE A  18 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3255)
  covalent geometry    : angle       0.61944 ( 4429)
  hydrogen bonds       : bond        0.04688 (  267)
  hydrogen bonds       : angle       4.21134 (  795)

********************** 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
  58 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 39
  time to evaluate  : 0.066 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.8453 (ttm) cc_final: 0.8226 (ttm)
REVERT: A  141 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6817 (mp)
REVERT: A  305 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8295 (mm)
REVERT: A  415 ARG cc_start: 0.5722 (ptm160) cc_final: 0.5481 (ptt90)
REVERT: A  418 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6804 (ttm170)
  outliers start: 19
  outliers final: 15
  residues processed: 54
  average time/residue: 0.0619
  time to fit residues: 4.0739
Evaluate side-chains
  57 residues out of total 334 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 39
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue   82 SER
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  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
Chi-restraints excluded: chain A residue  418 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0370
   chunk 2 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.6658

-------------------------------------------------------------------------------
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 = 0.4194 r_free = 0.4194 target = 0.203234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.163379 restraints weight = 3782.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.167587 restraints weight = 2245.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.170170 restraints weight = 1667.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.171495 restraints weight = 1413.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.171697 restraints weight = 1288.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3255  Z= 0.158
  Angle     :  0.627   8.382   4429  Z= 0.328
  Chirality :  0.039   0.163    500
  Planarity :  0.005   0.065    544
  Dihedral  :  4.220  17.006    441
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  4.38 %
    Favored  : 95.13 %
  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:  2.49 (0.43), residues: 411
  helix:  2.24 (0.28), residues: 331
  sheet:  None (None), residues: 0
  loop : -0.93 (0.75), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 300 
 TYR   0.016   0.001   TYR A  21 
 PHE   0.015   0.002   PHE A  18 
 TRP   0.011   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 3255)
  covalent geometry    : angle       0.62672 ( 4429)
  hydrogen bonds       : bond        0.04747 (  267)
  hydrogen bonds       : angle       4.22469 (  795)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 662.63 seconds
wall clock time: 12 minutes 4.97 seconds (724.97 seconds total)