Starting phenix.real_space_refine
on Fri Aug 22 13:30:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8goe_34176/08_2025/8goe_34176_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8goe_34176/08_2025/8goe_34176.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8goe_34176/08_2025/8goe_34176.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8goe_34176/08_2025/8goe_34176.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8goe_34176/08_2025/8goe_34176_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8goe_34176/08_2025/8goe_34176_neut.cif"
  }
  resolution = 3.0
  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=   0.005
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      10      5.16       5
     C    2204      2.51       5
     N     555      2.21       5
     O     554      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3323
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3290
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 407, 3268
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 14, 'TRANS': 392}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 407, 3268
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 14, 'TRANS': 392}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 3334
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 1, 33
          Unusual residues: {'THH': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AARG A 133 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 133 " occ=0.50
    residue:
      pdb=" N  AARG A 208 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 208 " occ=0.50
  Time building chain proxies: 1.82, per 1000 atoms: 0.55
  Number of scatterers: 3323
  At special positions: 0
  Unit cell: (78, 73, 67, 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      10     16.00
     O     554      8.00
     N     555      7.00
     C    2204      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: 0.28
  Conformation dependent library (CDL) restraints added in 257.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue is complicated and confusing
        pdb=" CB  THH A 601 "
  Number of C-beta restraints generated:  774

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 0 sheets defined
      82.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 39
      removed outlier: 3.754A  pdb=" N   TYR A  31 " --> pdb=" O   HIS A  27 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   PHE A  34 " --> pdb=" O   CYS A  30 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE A  37 " --> pdb=" O   CYS A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 53
    Processing helix  chain 'A' and resid 60 through 65
    Processing helix  chain 'A' and resid 68 through 90
      removed outlier: 3.778A  pdb=" N   LEU A  72 " --> pdb=" O   ILE A  68 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   SER A  73 " --> pdb=" O   THR A  69 " (cutoff:3.500A)
      removed outlier: 4.909A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      Proline residue:  A  82  - end of helix
      removed outlier: 3.662A  pdb=" N   ASP A  88 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 113
      removed outlier: 3.559A  pdb=" N   LEU A 111 " --> pdb=" O   TRP A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 132
      removed outlier: 3.596A  pdb=" N   THR A 129 " --> pdb=" O   PHE A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 138
      removed outlier: 4.280A  pdb=" N   SER A 137 " --> pdb=" O  AARG A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 144
      removed outlier: 3.611A  pdb=" N   SER A 142 " --> pdb=" O   SER A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 176
      removed outlier: 4.722A  pdb=" N   GLN A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
      removed outlier: 6.084A  pdb=" N   ARG A 151 " --> pdb=" O   ALA A 147 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL A 152 " --> pdb=" O   ARG A 148 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LEU A 162 " --> pdb=" O   ALA A 158 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   SER A 168 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL A 175 " --> pdb=" O   GLY A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 202
      removed outlier: 3.741A  pdb=" N   PHE A 202 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 257
    Processing helix  chain 'A' and resid 258 through 263
      removed outlier: 3.772A  pdb=" N   ARG A 263 " --> pdb=" O   GLY A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 277
      removed outlier: 3.741A  pdb=" N   LEU A 272 " --> pdb=" O   ARG A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 286
      removed outlier: 3.552A  pdb=" N   VAL A 284 " --> pdb=" O   GLY A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 296
    Processing helix  chain 'A' and resid 300 through 304
      removed outlier: 3.534A  pdb=" N   ARG A 303 " --> pdb=" O   ASN A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 325
      removed outlier: 3.624A  pdb=" N   SER A 313 " --> pdb=" O   ALA A 309 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   GLY A 325 " --> pdb=" O   SER A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 356
    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 388
      removed outlier: 3.517A  pdb=" N   PHE A 369 " --> pdb=" O   CYS A 365 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   PHE A 372 " --> pdb=" O   ALA A 368 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LEU A 379 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
      Proline residue:  A 381  - end of helix
    Processing helix  chain 'A' and resid 392 through 418
    Processing helix  chain 'A' and resid 427 through 453
      removed outlier: 3.607A  pdb=" N   LEU A 434 " --> pdb=" O   LYS A 430 " (cutoff:3.500A)

    215 hydrogen bonds defined for protein.
    642 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: 0.51

  Time building geometry restraints manager: 0.38 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 472
        1.31 -     1.43: 1057
        1.43 -     1.56: 1871
        1.56 -     1.68: 1
        1.68 -     1.81: 16
  Bond restraints: 3417
  Sorted by residual:
  bond pdb=" C4  THH A 601 "
       pdb=" O4  THH A 601 "
    ideal  model  delta    sigma   weight residual
    1.347  1.184  0.163 2.00e-02 2.50e+03 6.64e+01
  bond pdb=" N8  THH A 601 "
       pdb=" C8AATHH A 601 "
    ideal  model  delta    sigma   weight residual
    1.351  1.508 -0.157 2.00e-02 2.50e+03 6.13e+01
  bond pdb=" N   THH A 601 "
       pdb=" C   THH A 601 "
    ideal  model  delta    sigma   weight residual
    1.346  1.479 -0.133 2.00e-02 2.50e+03 4.45e+01
  bond pdb=" N5  THH A 601 "
       pdb=" C4AATHH A 601 "
    ideal  model  delta    sigma   weight residual
    1.419  1.504 -0.085 2.00e-02 2.50e+03 1.79e+01
  bond pdb=" C15 THH A 601 "
       pdb=" N10 THH A 601 "
    ideal  model  delta    sigma   weight residual
    1.379  1.460 -0.081 2.00e-02 2.50e+03 1.65e+01
  ... (remaining 3412 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 4505
        1.96 -     3.91: 117
        3.91 -     5.87: 24
        5.87 -     7.83: 12
        7.83 -     9.79: 1
  Bond angle restraints: 4659
  Sorted by residual:
  angle pdb=" C   TYR A  92 "
        pdb=" CA  TYR A  92 "
        pdb=" CB  TYR A  92 "
      ideal   model   delta    sigma   weight residual
     111.23  101.44    9.79 1.63e+00 3.76e-01 3.60e+01
  angle pdb=" N   GLN A 120 "
        pdb=" CA  GLN A 120 "
        pdb=" C   GLN A 120 "
      ideal   model   delta    sigma   weight residual
     111.36  105.80    5.56 1.09e+00 8.42e-01 2.60e+01
  angle pdb=" CA  VAL A 327 "
        pdb=" CB  VAL A 327 "
        pdb=" CG1 VAL A 327 "
      ideal   model   delta    sigma   weight residual
     110.40  115.30   -4.90 1.70e+00 3.46e-01 8.30e+00
  angle pdb=" N   THR A  69 "
        pdb=" CA  THR A  69 "
        pdb=" C   THR A  69 "
      ideal   model   delta    sigma   weight residual
     109.81  115.98   -6.17 2.21e+00 2.05e-01 7.79e+00
  angle pdb=" CA  THR A  49 "
        pdb=" C   THR A  49 "
        pdb=" N   PRO A  50 "
      ideal   model   delta    sigma   weight residual
     118.44  122.66   -4.22 1.59e+00 3.96e-01 7.06e+00
  ... (remaining 4654 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.92: 1687
       11.92 -    23.84: 206
       23.84 -    35.75: 57
       35.75 -    47.67: 15
       47.67 -    59.59: 18
  Dihedral angle restraints: 1983
    sinusoidal: 777
      harmonic: 1206
  Sorted by residual:
  dihedral pdb=" CA  ARG A  91 "
           pdb=" C   ARG A  91 "
           pdb=" N   TYR A  92 "
           pdb=" CA  TYR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.86   25.14     0      5.00e+00 4.00e-02 2.53e+01
  dihedral pdb=" CA  LEU A 452 "
           pdb=" C   LEU A 452 "
           pdb=" N   ASP A 453 "
           pdb=" CA  ASP A 453 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.97   18.03     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CG  ARG A 253 "
           pdb=" CD  ARG A 253 "
           pdb=" NE  ARG A 253 "
           pdb=" CZ  ARG A 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.63  -43.63     2      1.50e+01 4.44e-03 1.02e+01
  ... (remaining 1980 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 345
       0.039 -    0.077: 151
       0.077 -    0.116: 29
       0.116 -    0.155: 8
       0.155 -    0.193: 4
  Chirality restraints: 537
  Sorted by residual:
  chirality pdb=" CA  ARG A  42 "
            pdb=" N   ARG A  42 "
            pdb=" C   ARG A  42 "
            pdb=" CB  ARG A  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.34e-01
  chirality pdb=" CA  LEU A 121 "
            pdb=" N   LEU A 121 "
            pdb=" C   LEU A 121 "
            pdb=" CB  LEU A 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.39e-01
  chirality pdb=" CA  MET A 122 "
            pdb=" N   MET A 122 "
            pdb=" C   MET A 122 "
            pdb=" CB  MET A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.17 2.00e-01 2.50e+01 7.65e-01
  ... (remaining 534 not shown)

  Planarity restraints: 565
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  69 "    0.041 5.00e-02 4.00e+02   6.10e-02 5.96e+00
        pdb=" N   PRO A  70 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A  70 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A  70 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  41 "    0.010 2.00e-02 2.50e+03   2.11e-02 4.44e+00
        pdb=" C   ILE A  41 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   ILE A  41 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ARG A  42 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  81 "   -0.035 5.00e-02 4.00e+02   5.22e-02 4.36e+00
        pdb=" N   PRO A  82 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A  82 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  82 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 562 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 997
        2.80 -     3.32: 2989
        3.32 -     3.85: 5671
        3.85 -     4.37: 7086
        4.37 -     4.90: 11737
  Nonbonded interactions: 28480
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A  42 "
            pdb=" OE2 GLU A  45 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" O   VAL A 304 "
            pdb=" OH  TYR A 366 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   VAL A  64 "
            pdb=" OG1 THR A  69 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   LEU A  32 "
            pdb=" OH  TYR A 136 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" OE2 GLU A  45 "
            pdb=" OH  TYR A 126 "
     model   vdw
     2.313 3.040
  ... (remaining 28475 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=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             2.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.520
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
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      :  0.008   0.163   3417  Z= 0.367
  Angle     :  0.851   9.785   4659  Z= 0.468
  Chirality :  0.046   0.193    537
  Planarity :  0.006   0.061    565
  Dihedral  : 13.131  59.587   1209
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  8.50 %
    Favored  : 90.93 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -6.19 (0.23), residues: 409
  helix: -4.26 (0.12), residues: 323
  sheet:  None (None), residues: 0
  loop : -2.02 (0.53), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 214 
 TYR   0.008   0.001   TYR A  92 
 PHE   0.010   0.002   PHE A  37 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00751 ( 3417)
  covalent geometry    : angle       0.85131 ( 4659)
  hydrogen bonds       : bond        0.26976 (  215)
  hydrogen bonds       : angle      10.76877 (  642)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A   88 ASP cc_start: 0.8379 (t70) cc_final: 0.8063 (t70)
REVERT: A  294 GLU cc_start: 0.8068 (tt0) cc_final: 0.7688 (tt0)
REVERT: A  445 ILE cc_start: 0.8561 (mt) cc_final: 0.8268 (mt)
REVERT: A  452 LEU cc_start: 0.7280 (mt) cc_final: 0.7038 (mt)
  outliers start: 2
  outliers final: 1
  residues processed: 54
  average time/residue: 0.5569
  time to fit residues: 30.9770
Evaluate side-chains
  36 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 35
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.3980
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   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  99 GLN
A 266 GLN
A 277 ASN
A 377 GLN
A 431 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.098184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.078810 restraints weight = 18386.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.2773 rms_B_bonded: 3.15
r_work: 0.2594 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2616
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2616 r_free = 0.2616    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2616 r_free = 0.2616    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2616
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3417  Z= 0.146
  Angle     :  0.564   9.054   4659  Z= 0.291
  Chirality :  0.038   0.105    537
  Planarity :  0.005   0.036    565
  Dihedral  :  7.423  57.444    493
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 10.20 %
    Favored  : 88.95 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.65 (0.34), residues: 409
  helix: -1.55 (0.24), residues: 322
  sheet:  None (None), residues: 0
  loop : -1.73 (0.55), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 333 
 TYR   0.010   0.001   TYR A 149 
 PHE   0.015   0.001   PHE A 372 
 TRP   0.012   0.002   TRP A 107 
 HIS   0.002   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 3417)
  covalent geometry    : angle       0.56354 ( 4659)
  hydrogen bonds       : bond        0.04083 (  215)
  hydrogen bonds       : angle       4.85051 (  642)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7030 (mm)
REVERT: A  294 GLU cc_start: 0.8407 (tt0) cc_final: 0.8006 (tt0)
REVERT: A  452 LEU cc_start: 0.6955 (mt) cc_final: 0.6729 (mt)
  outliers start: 3
  outliers final: 0
  residues processed: 41
  average time/residue: 0.4622
  time to fit residues: 19.7454
Evaluate side-chains
  37 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0370
   chunk 26 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.6858

-------------------------------------------------------------------------------
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 = 0.3039 r_free = 0.3039 target = 0.096956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.078281 restraints weight = 13585.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.2771 rms_B_bonded: 2.74
r_work: 0.2604 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2663
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2663
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3417  Z= 0.149
  Angle     :  0.532   7.987   4659  Z= 0.269
  Chirality :  0.038   0.107    537
  Planarity :  0.004   0.029    565
  Dihedral  :  6.775  50.698    492
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 10.76 %
    Favored  : 88.10 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.39), residues: 409
  helix:  0.00 (0.28), residues: 317
  sheet:  None (None), residues: 0
  loop : -1.32 (0.54), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 333 
 TYR   0.010   0.001   TYR A 149 
 PHE   0.025   0.001   PHE A 322 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 3417)
  covalent geometry    : angle       0.53167 ( 4659)
  hydrogen bonds       : bond        0.03847 (  215)
  hydrogen bonds       : angle       4.40501 (  642)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A  161 LEU cc_start: 0.7700 (pp) cc_final: 0.7319 (mp)
REVERT: A  294 GLU cc_start: 0.8445 (tt0) cc_final: 0.8014 (tt0)
  outliers start: 4
  outliers final: 3
  residues processed: 43
  average time/residue: 0.4863
  time to fit residues: 21.7168
Evaluate side-chains
  39 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  251 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 6 optimal weight:    0.3980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.8186

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.104090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.084366 restraints weight = 18758.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.2768 rms_B_bonded: 3.06
r_work: 0.2591 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2591
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2576
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2576 r_free = 0.2576    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2576 r_free = 0.2576    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2576
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3417  Z= 0.165
  Angle     :  0.548   9.352   4659  Z= 0.273
  Chirality :  0.039   0.114    537
  Planarity :  0.003   0.026    565
  Dihedral  :  6.521  46.399    492
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 11.90 %
    Favored  : 86.97 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.40), residues: 409
  helix:  0.49 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.09 (0.57), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 333 
 TYR   0.011   0.001   TYR A 149 
 PHE   0.013   0.001   PHE A 372 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 3417)
  covalent geometry    : angle       0.54807 ( 4659)
  hydrogen bonds       : bond        0.03833 (  215)
  hydrogen bonds       : angle       4.30842 (  642)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A  161 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7445 (mp)
REVERT: A  294 GLU cc_start: 0.8664 (tt0) cc_final: 0.8222 (tt0)
  outliers start: 4
  outliers final: 1
  residues processed: 36
  average time/residue: 0.4682
  time to fit residues: 17.5883
Evaluate side-chains
  35 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  175 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3029 r_free = 0.3029 target = 0.096506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.077449 restraints weight = 14088.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 2.72
r_work: 0.2693 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2627
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2627 r_free = 0.2627    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2627 r_free = 0.2627    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2627
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3417  Z= 0.154
  Angle     :  0.539   9.335   4659  Z= 0.267
  Chirality :  0.039   0.120    537
  Planarity :  0.004   0.035    565
  Dihedral  :  6.300  43.689    492
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 11.90 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.41), residues: 409
  helix:  0.79 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -0.88 (0.59), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 256 
 TYR   0.010   0.001   TYR A 149 
 PHE   0.026   0.001   PHE A 322 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 3417)
  covalent geometry    : angle       0.53911 ( 4659)
  hydrogen bonds       : bond        0.03739 (  215)
  hydrogen bonds       : angle       4.21171 (  642)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 34
  time to evaluate  : 0.103 
Fit side-chains
REVERT: A  161 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7393 (mm)
REVERT: A  294 GLU cc_start: 0.8671 (tt0) cc_final: 0.8349 (tt0)
  outliers start: 5
  outliers final: 3
  residues processed: 38
  average time/residue: 0.4240
  time to fit residues: 16.7079
Evaluate side-chains
  39 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0670
   chunk 32 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
A 346 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.098033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.078718 restraints weight = 15470.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 2.85
r_work: 0.2709 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2657
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2657 r_free = 0.2657    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2657 r_free = 0.2657    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2657
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3417  Z= 0.122
  Angle     :  0.519  10.353   4659  Z= 0.255
  Chirality :  0.038   0.111    537
  Planarity :  0.003   0.025    565
  Dihedral  :  5.917  39.785    492
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 11.90 %
    Favored  : 86.97 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.41), residues: 409
  helix:  1.03 (0.29), residues: 323
  sheet:  None (None), residues: 0
  loop : -0.74 (0.62), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 256 
 TYR   0.009   0.001   TYR A 149 
 PHE   0.014   0.001   PHE A 372 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.001   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3417)
  covalent geometry    : angle       0.51939 ( 4659)
  hydrogen bonds       : bond        0.03557 (  215)
  hydrogen bonds       : angle       4.04378 (  642)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7386 (mm)
REVERT: A  294 GLU cc_start: 0.8652 (tt0) cc_final: 0.8346 (tt0)
REVERT: A  330 ARG cc_start: 0.7756 (mtm110) cc_final: 0.7494 (mtm-85)
  outliers start: 4
  outliers final: 2
  residues processed: 38
  average time/residue: 0.3719
  time to fit residues: 14.6677
Evaluate side-chains
  38 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0020
   chunk 39 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0870
   chunk 1 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.3966

-------------------------------------------------------------------------------
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 = 0.3071 r_free = 0.3071 target = 0.099595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.080288 restraints weight = 16075.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 2.92
r_work: 0.2673 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2679
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2679 r_free = 0.2679    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2679 r_free = 0.2679    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2679
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3417  Z= 0.111
  Angle     :  0.504  10.334   4659  Z= 0.247
  Chirality :  0.037   0.111    537
  Planarity :  0.003   0.028    565
  Dihedral  :  5.547  36.494    492
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 12.18 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.41), residues: 409
  helix:  1.33 (0.29), residues: 322
  sheet:  None (None), residues: 0
  loop : -0.72 (0.61), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 256 
 TYR   0.011   0.001   TYR A 155 
 PHE   0.025   0.001   PHE A 322 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 3417)
  covalent geometry    : angle       0.50428 ( 4659)
  hydrogen bonds       : bond        0.03432 (  215)
  hydrogen bonds       : angle       3.89846 (  642)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A  161 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7180 (mm)
REVERT: A  294 GLU cc_start: 0.8593 (tt0) cc_final: 0.8248 (tt0)
REVERT: A  330 ARG cc_start: 0.7617 (mtm110) cc_final: 0.7403 (mtm-85)
  outliers start: 4
  outliers final: 2
  residues processed: 43
  average time/residue: 0.4038
  time to fit residues: 17.9895
Evaluate side-chains
  38 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 21 optimal weight:    0.3980
   chunk 6 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3031 r_free = 0.3031 target = 0.097209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.076344 restraints weight = 18605.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.2782 rms_B_bonded: 3.38
r_work: 0.2583 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2583
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2725
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3417  Z= 0.161
  Angle     :  0.569   9.599   4659  Z= 0.279
  Chirality :  0.040   0.116    537
  Planarity :  0.005   0.086    565
  Dihedral  :  5.795  35.598    492
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 13.60 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.41), residues: 409
  helix:  1.29 (0.29), residues: 323
  sheet:  None (None), residues: 0
  loop : -0.64 (0.63), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A 456 
 TYR   0.011   0.001   TYR A 149 
 PHE   0.012   0.001   PHE A 372 
 TRP   0.011   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 3417)
  covalent geometry    : angle       0.56905 ( 4659)
  hydrogen bonds       : bond        0.03693 (  215)
  hydrogen bonds       : angle       4.03511 (  642)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.072 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7326 (mm)
REVERT: A  294 GLU cc_start: 0.8644 (tt0) cc_final: 0.8308 (tt0)
  outliers start: 3
  outliers final: 2
  residues processed: 38
  average time/residue: 0.3344
  time to fit residues: 13.1998
Evaluate side-chains
  38 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 20 optimal weight:    0.3980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.098108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.077344 restraints weight = 17983.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 3.33
r_work: 0.2757 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2746
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2746 r_free = 0.2746    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2746 r_free = 0.2746    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2746
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3417  Z= 0.140
  Angle     :  0.551   9.230   4659  Z= 0.270
  Chirality :  0.039   0.112    537
  Planarity :  0.005   0.083    565
  Dihedral  :  5.652  35.089    492
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 13.60 %
    Favored  : 85.27 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.42), residues: 409
  helix:  1.39 (0.29), residues: 323
  sheet:  None (None), residues: 0
  loop : -0.63 (0.63), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A 456 
 TYR   0.011   0.001   TYR A 155 
 PHE   0.028   0.001   PHE A 322 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3417)
  covalent geometry    : angle       0.55061 ( 4659)
  hydrogen bonds       : bond        0.03585 (  215)
  hydrogen bonds       : angle       3.95138 (  642)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A  161 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7388 (mm)
REVERT: A  294 GLU cc_start: 0.8647 (tt0) cc_final: 0.8332 (tt0)
  outliers start: 4
  outliers final: 2
  residues processed: 37
  average time/residue: 0.3384
  time to fit residues: 13.0924
Evaluate side-chains
  36 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0670
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 33 optimal weight:    0.3980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.4918

-------------------------------------------------------------------------------
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 = 0.3058 r_free = 0.3058 target = 0.099013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.078576 restraints weight = 15117.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 3.10
r_work: 0.2782 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3417  Z= 0.125
  Angle     :  0.540   9.204   4659  Z= 0.265
  Chirality :  0.038   0.114    537
  Planarity :  0.005   0.080    565
  Dihedral  :  5.496  33.746    492
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 13.60 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.42), residues: 409
  helix:  1.52 (0.29), residues: 323
  sheet:  None (None), residues: 0
  loop : -0.58 (0.63), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A 456 
 TYR   0.009   0.001   TYR A 149 
 PHE   0.013   0.001   PHE A 372 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3417)
  covalent geometry    : angle       0.54022 ( 4659)
  hydrogen bonds       : bond        0.03509 (  215)
  hydrogen bonds       : angle       3.87320 (  642)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A  161 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7362 (mm)
REVERT: A  294 GLU cc_start: 0.8624 (tt0) cc_final: 0.8303 (tt0)
REVERT: A  393 LYS cc_start: 0.8241 (mmtm) cc_final: 0.7961 (tppp)
  outliers start: 3
  outliers final: 2
  residues processed: 35
  average time/residue: 0.3854
  time to fit residues: 14.0509
Evaluate side-chains
  36 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  415 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 11 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 9 optimal weight:    0.4980
   chunk 27 optimal weight:    0.4980
   chunk 22 optimal weight:    0.3980
   chunk 12 optimal weight:    0.1980
   chunk 24 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0870
   overall best weight:    0.3358

-------------------------------------------------------------------------------
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 = 0.3079 r_free = 0.3079 target = 0.100446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.079960 restraints weight = 17816.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.2832 rms_B_bonded: 3.15
r_work: 0.2642 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2768
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2768 r_free = 0.2768    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2768 r_free = 0.2768    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2768
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   3417  Z= 0.110
  Angle     :  0.523   9.090   4659  Z= 0.256
  Chirality :  0.037   0.115    537
  Planarity :  0.005   0.078    565
  Dihedral  :  5.272  31.093    492
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 14.45 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.42), residues: 409
  helix:  1.68 (0.29), residues: 322
  sheet:  None (None), residues: 0
  loop : -0.53 (0.63), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 456 
 TYR   0.011   0.001   TYR A 155 
 PHE   0.027   0.001   PHE A 322 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 3417)
  covalent geometry    : angle       0.52303 ( 4659)
  hydrogen bonds       : bond        0.03390 (  215)
  hydrogen bonds       : angle       3.76243 (  642)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1112.32 seconds
wall clock time: 19 minutes 49.65 seconds (1189.65 seconds total)