Starting phenix.real_space_refine
on Wed Sep 17 03:23:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z7y_39832/09_2025/8z7y_39832.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z7y_39832/09_2025/8z7y_39832.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z7y_39832/09_2025/8z7y_39832.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z7y_39832/09_2025/8z7y_39832.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z7y_39832/09_2025/8z7y_39832.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z7y_39832/09_2025/8z7y_39832.map"
  }
  resolution = 3.02
  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=   0.157
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      16      5.16       5
     C    2082      2.51       5
     N     463      2.21       5
     O     522      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3083
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3046
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 3046
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 13, 'TRANS': 368}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 37
          Unusual residues: {'2TA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.90, per 1000 atoms: 0.29
  Number of scatterers: 3083
  At special positions: 0
  Unit cell: (82.948, 58.716, 69.9, 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      16     16.00
     O     522      8.00
     N     463      7.00
     C    2082      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: 0.39
  Conformation dependent library (CDL) restraints added in 123.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  724

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 0 sheets defined
      84.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 28
      removed outlier: 3.647A  pdb=" N   VAL A  17 " --> pdb=" O   ILE A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 40
    Processing helix  chain 'A' and resid 47 through 54
    Processing helix  chain 'A' and resid 56 through 77
      removed outlier: 4.098A  pdb=" N   THR A  60 " --> pdb=" O   PHE A  56 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   TYR A  61 " --> pdb=" O   PRO A  57 " (cutoff:3.500A)
      removed outlier: 4.923A  pdb=" N   LEU A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
      Proline residue:  A  69  - end of helix
      removed outlier: 3.716A  pdb=" N   ASP A  75 " --> pdb=" O   PHE A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 99
      removed outlier: 3.645A  pdb=" N   ILE A  83 " --> pdb=" O   TYR A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 131
      removed outlier: 4.523A  pdb=" N   VAL A 121 " --> pdb=" O   THR A 117 " (cutoff:3.500A)
      removed outlier: 5.340A  pdb=" N   ALA A 122 " --> pdb=" O   ALA A 118 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   TYR A 123 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   TYR A 124 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ILE A 127 " --> pdb=" O   TYR A 123 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   TYR A 128 " --> pdb=" O   TYR A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 166
      removed outlier: 3.573A  pdb=" N   ASN A 166 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 189
      removed outlier: 4.254A  pdb=" N   PHE A 189 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 307
      removed outlier: 4.240A  pdb=" N   TRP A 281 " --> pdb=" O   ARG A 277 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   TYR A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   GLN A 300 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
      removed outlier: 5.757A  pdb=" N   ILE A 301 " --> pdb=" O   ASN A 297 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LYS A 306 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ALA A 307 " --> pdb=" O   TRP A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 337
      removed outlier: 4.015A  pdb=" N   GLY A 335 " --> pdb=" O   ALA A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 366
    Processing helix  chain 'A' and resid 368 through 396
    Processing helix  chain 'A' and resid 399 through 426
      removed outlier: 3.987A  pdb=" N   ALA A 404 " --> pdb=" O   VAL A 400 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU A 405 " --> pdb=" O   GLU A 401 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ILE A 409 " --> pdb=" O   LEU A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 456
      removed outlier: 3.791A  pdb=" N   PHE A 439 " --> pdb=" O   VAL A 435 " (cutoff:3.500A)
      removed outlier: 5.508A  pdb=" N   LEU A 440 " --> pdb=" O   SER A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 465
      removed outlier: 4.276A  pdb=" N   TYR A 462 " --> pdb=" O   MET A 458 " (cutoff:3.500A)

    231 hydrogen bonds defined for protein.
    693 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: 0.33

  Time building geometry restraints manager: 0.39 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 440
        1.30 -     1.43: 942
        1.43 -     1.56: 1763
        1.56 -     1.69: 2
        1.69 -     1.81: 29
  Bond restraints: 3176
  Sorted by residual:
  bond pdb=" CAO 2TA A 501 "
       pdb=" NAP 2TA A 501 "
    ideal  model  delta    sigma   weight residual
    1.444  1.173  0.271 2.00e-02 2.50e+03 1.83e+02
  bond pdb=" CAS 2TA A 501 "
       pdb=" CAT 2TA A 501 "
    ideal  model  delta    sigma   weight residual
    1.532  1.323  0.209 2.00e-02 2.50e+03 1.09e+02
  bond pdb=" CAQ 2TA A 501 "
       pdb=" NAP 2TA A 501 "
    ideal  model  delta    sigma   weight residual
    1.454  1.256  0.198 2.00e-02 2.50e+03 9.77e+01
  bond pdb=" C2  2TA A 501 "
       pdb=" N1  2TA A 501 "
    ideal  model  delta    sigma   weight residual
    1.322  1.487 -0.165 2.00e-02 2.50e+03 6.79e+01
  bond pdb=" CAY 2TA A 501 "
       pdb=" CAZ 2TA A 501 "
    ideal  model  delta    sigma   weight residual
    1.386  1.536 -0.150 2.00e-02 2.50e+03 5.60e+01
  ... (remaining 3171 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.25: 4301
        3.25 -     6.50: 36
        6.50 -     9.75: 0
        9.75 -    13.00: 1
       13.00 -    16.25: 2
  Bond angle restraints: 4340
  Sorted by residual:
  angle pdb=" OBJ 2TA A 501 "
        pdb=" SBD 2TA A 501 "
        pdb=" OBK 2TA A 501 "
      ideal   model   delta    sigma   weight residual
     118.13  101.88   16.25 3.00e+00 1.11e-01 2.94e+01
  angle pdb=" C4  2TA A 501 "
        pdb=" NAW 2TA A 501 "
        pdb=" CAX 2TA A 501 "
      ideal   model   delta    sigma   weight residual
     131.24  116.51   14.73 3.00e+00 1.11e-01 2.41e+01
  angle pdb=" C2  2TA A 501 "
        pdb=" NAF 2TA A 501 "
        pdb=" CAG 2TA A 501 "
      ideal   model   delta    sigma   weight residual
     131.32  119.61   11.71 3.00e+00 1.11e-01 1.52e+01
  angle pdb=" N   PRO A 191 "
        pdb=" CA  PRO A 191 "
        pdb=" CB  PRO A 191 "
      ideal   model   delta    sigma   weight residual
     103.35  105.90   -2.55 8.70e-01 1.32e+00 8.57e+00
  angle pdb=" N   TYR A 126 "
        pdb=" CA  TYR A 126 "
        pdb=" C   TYR A 126 "
      ideal   model   delta    sigma   weight residual
     111.28  108.30    2.98 1.09e+00 8.42e-01 7.50e+00
  ... (remaining 4335 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.64: 1749
       33.64 -    67.28: 43
       67.28 -   100.92: 5
      100.92 -   134.56: 1
      134.56 -   168.19: 1
  Dihedral angle restraints: 1799
    sinusoidal: 665
      harmonic: 1134
  Sorted by residual:
  dihedral pdb=" CA  ARG A  78 "
           pdb=" C   ARG A  78 "
           pdb=" N   TYR A  79 "
           pdb=" CA  TYR A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.87   23.13     0      5.00e+00 4.00e-02 2.14e+01
  dihedral pdb=" CAG 2TA A 501 "
           pdb=" C2  2TA A 501 "
           pdb=" NAF 2TA A 501 "
           pdb=" N1  2TA A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -0.72 -168.91  168.19     1      3.00e+01 1.11e-03 2.11e+01
  dihedral pdb=" CAI 2TA A 501 "
           pdb=" CAJ 2TA A 501 "
           pdb=" OAM 2TA A 501 "
           pdb=" CAN 2TA A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -1.36 -123.50  122.14     1      3.00e+01 1.11e-03 1.63e+01
  ... (remaining 1796 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 381
       0.047 -    0.095: 96
       0.095 -    0.142: 18
       0.142 -    0.190: 2
       0.190 -    0.237: 1
  Chirality restraints: 498
  Sorted by residual:
  chirality pdb=" CB  VAL A  77 "
            pdb=" CA  VAL A  77 "
            pdb=" CG1 VAL A  77 "
            pdb=" CG2 VAL A  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CB  VAL A 109 "
            pdb=" CA  VAL A 109 "
            pdb=" CG1 VAL A 109 "
            pdb=" CG2 VAL A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.68e-01
  chirality pdb=" CA  PHE A  56 "
            pdb=" N   PHE A  56 "
            pdb=" C   PHE A  56 "
            pdb=" CB  PHE A  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.15e-01
  ... (remaining 495 not shown)

  Planarity restraints: 516
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  56 "   -0.009 2.00e-02 2.50e+03   9.40e-03 1.55e+00
        pdb=" CG  PHE A  56 "    0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  56 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  56 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  56 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  56 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  56 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 393 "   -0.005 2.00e-02 2.50e+03   1.08e-02 1.16e+00
        pdb=" CD  GLN A 393 "    0.019 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 393 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 393 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A  36 "    0.018 5.00e-02 4.00e+02   2.68e-02 1.15e+00
        pdb=" N   PRO A  37 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO A  37 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A  37 "    0.015 5.00e-02 4.00e+02
  ... (remaining 513 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 424
        2.75 -     3.29: 3215
        3.29 -     3.83: 5427
        3.83 -     4.36: 6289
        4.36 -     4.90: 10948
  Nonbonded interactions: 26303
  Sorted by model distance:
  nonbonded pdb=" O   PHE A  25 "
            pdb=" OG  SER A 179 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   SER A  26 "
            pdb=" NH1 ARG A  29 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" NH1 ARG A 277 "
            pdb=" OH  TYR A 280 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" O   MET A 192 "
            pdb=" NZ  LYS A 194 "
     model   vdw
     2.355 3.120
  nonbonded pdb=" NE2 GLN A 159 "
            pdb=" OG  SER A 163 "
     model   vdw
     2.368 3.120
  ... (remaining 26298 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 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:             1.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.750
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6489
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      :  0.013   0.271   3176  Z= 0.670
  Angle     :  0.799  16.255   4340  Z= 0.388
  Chirality :  0.044   0.237    498
  Planarity :  0.004   0.027    516
  Dihedral  : 16.151 168.195   1075
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.44), residues: 378
  helix:  1.18 (0.30), residues: 302
  sheet:  None (None), residues: 0
  loop : -1.01 (0.72), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  78 
 TYR   0.012   0.001   TYR A 151 
 PHE   0.022   0.002   PHE A  56 
 TRP   0.011   0.002   TRP A  94 
 HIS   0.003   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.01342 ( 3176)
  covalent geometry    : angle       0.79903 ( 4340)
  hydrogen bonds       : bond        0.10750 (  231)
  hydrogen bonds       : angle       4.55549 (  693)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.111 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.0412
  time to fit residues: 2.5142
Evaluate side-chains
  38 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.2980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.4980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
A 300 GLN
A 316 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.210344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.186757 restraints weight = 3329.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.4082 rms_B_bonded: 1.54
r_work: 0.3994 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3865 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6649
moved from start:          0.0990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3176  Z= 0.143
  Angle     :  0.557   5.353   4340  Z= 0.287
  Chirality :  0.041   0.151    498
  Planarity :  0.004   0.036    516
  Dihedral  : 12.380 156.066    434
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  :  5.50 %
    Favored  : 93.27 %
  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 aren not related in a simple way.
  whole:  1.05 (0.44), residues: 378
  helix:  1.13 (0.30), residues: 306
  sheet:  None (None), residues: 0
  loop : -0.93 (0.75), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 277 
 TYR   0.009   0.001   TYR A  38 
 PHE   0.014   0.002   PHE A  56 
 TRP   0.014   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 3176)
  covalent geometry    : angle       0.55674 ( 4340)
  hydrogen bonds       : bond        0.04073 (  231)
  hydrogen bonds       : angle       3.94821 (  693)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.063 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 43
  average time/residue: 0.0391
  time to fit residues: 2.3766
Evaluate side-chains
  44 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 41
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 300 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.206193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.182311 restraints weight = 3291.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.4040 rms_B_bonded: 1.54
r_work: 0.3950 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3823 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6703
moved from start:          0.1217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3176  Z= 0.168
  Angle     :  0.589   5.390   4340  Z= 0.302
  Chirality :  0.042   0.151    498
  Planarity :  0.004   0.037    516
  Dihedral  : 10.492 137.076    434
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  9.17 %
    Favored  : 88.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.44), residues: 378
  helix:  1.07 (0.30), residues: 307
  sheet:  None (None), residues: 0
  loop : -0.83 (0.77), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  78 
 TYR   0.010   0.002   TYR A  14 
 PHE   0.016   0.002   PHE A  56 
 TRP   0.014   0.002   TRP A  94 
 HIS   0.003   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 3176)
  covalent geometry    : angle       0.58926 ( 4340)
  hydrogen bonds       : bond        0.04172 (  231)
  hydrogen bonds       : angle       4.02666 (  693)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.119 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 42
  average time/residue: 0.0383
  time to fit residues: 2.3597
Evaluate side-chains
  43 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.205551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.181695 restraints weight = 3298.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.4053 rms_B_bonded: 1.52
r_work: 0.3957 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3828 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6731
moved from start:          0.1422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3176  Z= 0.171
  Angle     :  0.614   8.210   4340  Z= 0.307
  Chirality :  0.042   0.152    498
  Planarity :  0.004   0.038    516
  Dihedral  : 10.231 135.971    434
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.07 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.43), residues: 378
  helix:  1.02 (0.29), residues: 307
  sheet:  None (None), residues: 0
  loop : -0.80 (0.75), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 277 
 TYR   0.011   0.002   TYR A 126 
 PHE   0.012   0.002   PHE A  56 
 TRP   0.015   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 3176)
  covalent geometry    : angle       0.61412 ( 4340)
  hydrogen bonds       : bond        0.04134 (  231)
  hydrogen bonds       : angle       4.03875 (  693)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A   97 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6507 (mp)
REVERT: A  136 TYR cc_start: 0.5621 (m-80) cc_final: 0.4916 (m-80)
REVERT: A  320 GLU cc_start: 0.7098 (tt0) cc_final: 0.6805 (tt0)
  outliers start: 7
  outliers final: 5
  residues processed: 49
  average time/residue: 0.0420
  time to fit residues: 2.8662
Evaluate side-chains
  48 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 13 optimal weight:    0.1980
   chunk 14 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0870
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.4358

-------------------------------------------------------------------------------
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 = 0.4318 r_free = 0.4318 target = 0.211293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.187254 restraints weight = 3264.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 1.55
r_work: 0.3987 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3860 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6665
moved from start:          0.1476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3176  Z= 0.124
  Angle     :  0.541   7.142   4340  Z= 0.271
  Chirality :  0.040   0.139    498
  Planarity :  0.004   0.037    516
  Dihedral  : 10.234 137.838    434
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.07 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.44), residues: 378
  helix:  1.30 (0.30), residues: 306
  sheet:  None (None), residues: 0
  loop : -0.76 (0.78), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 277 
 TYR   0.019   0.001   TYR A  79 
 PHE   0.008   0.001   PHE A 279 
 TRP   0.016   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3176)
  covalent geometry    : angle       0.54097 ( 4340)
  hydrogen bonds       : bond        0.03618 (  231)
  hydrogen bonds       : angle       3.84229 (  693)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A  305 TYR cc_start: 0.6242 (m-10) cc_final: 0.5938 (t80)
REVERT: A  396 VAL cc_start: 0.4487 (OUTLIER) cc_final: 0.3956 (m)
  outliers start: 7
  outliers final: 5
  residues processed: 44
  average time/residue: 0.0384
  time to fit residues: 2.4180
Evaluate side-chains
  45 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  421 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0870
   chunk 14 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 17 optimal weight:    0.2980
   chunk 4 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.5358

-------------------------------------------------------------------------------
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 = 0.4285 r_free = 0.4285 target = 0.208879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.184793 restraints weight = 3259.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.4064 rms_B_bonded: 1.53
r_work: 0.3970 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3843 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6688
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3176  Z= 0.133
  Angle     :  0.551   6.391   4340  Z= 0.277
  Chirality :  0.040   0.148    498
  Planarity :  0.004   0.037    516
  Dihedral  : 10.107 136.272    434
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.29 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.44), residues: 378
  helix:  1.32 (0.30), residues: 307
  sheet:  None (None), residues: 0
  loop : -0.58 (0.78), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  78 
 TYR   0.015   0.001   TYR A  79 
 PHE   0.008   0.001   PHE A 189 
 TRP   0.014   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3176)
  covalent geometry    : angle       0.55097 ( 4340)
  hydrogen bonds       : bond        0.03696 (  231)
  hydrogen bonds       : angle       3.85156 (  693)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A   20 CYS cc_start: 0.5731 (t) cc_final: 0.5015 (m)
REVERT: A   97 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6628 (mp)
REVERT: A  305 TYR cc_start: 0.6348 (m-10) cc_final: 0.5931 (t80)
REVERT: A  396 VAL cc_start: 0.4450 (OUTLIER) cc_final: 0.3972 (m)
  outliers start: 8
  outliers final: 6
  residues processed: 45
  average time/residue: 0.0409
  time to fit residues: 2.6463
Evaluate side-chains
  47 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  421 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0980
   chunk 35 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   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 = 0.4284 r_free = 0.4284 target = 0.208414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.183996 restraints weight = 3279.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.4074 rms_B_bonded: 1.54
r_work: 0.3981 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3851 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6714
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3176  Z= 0.142
  Angle     :  0.559   5.864   4340  Z= 0.282
  Chirality :  0.040   0.152    498
  Planarity :  0.004   0.037    516
  Dihedral  : 10.034 135.022    434
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.90 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.38 (0.44), residues: 378
  helix:  1.30 (0.30), residues: 307
  sheet:  None (None), residues: 0
  loop : -0.56 (0.78), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  78 
 TYR   0.014   0.001   TYR A  79 
 PHE   0.009   0.001   PHE A 189 
 TRP   0.014   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 3176)
  covalent geometry    : angle       0.55937 ( 4340)
  hydrogen bonds       : bond        0.03780 (  231)
  hydrogen bonds       : angle       3.88583 (  693)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.093 
Fit side-chains
REVERT: A   20 CYS cc_start: 0.5750 (t) cc_final: 0.5020 (m)
REVERT: A   97 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6676 (mp)
REVERT: A  305 TYR cc_start: 0.6240 (m-10) cc_final: 0.5939 (t80)
  outliers start: 8
  outliers final: 6
  residues processed: 47
  average time/residue: 0.0348
  time to fit residues: 2.3446
Evaluate side-chains
  47 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  421 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4307 r_free = 0.4307 target = 0.209445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.184937 restraints weight = 3321.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.4090 rms_B_bonded: 1.58
r_work: 0.3998 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3870 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6725
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3176  Z= 0.151
  Angle     :  0.569   5.534   4340  Z= 0.287
  Chirality :  0.041   0.160    498
  Planarity :  0.004   0.038    516
  Dihedral  : 10.015 134.556    434
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.90 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.44), residues: 378
  helix:  1.28 (0.30), residues: 307
  sheet:  None (None), residues: 0
  loop : -0.49 (0.78), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 277 
 TYR   0.013   0.001   TYR A  79 
 PHE   0.009   0.002   PHE A 189 
 TRP   0.013   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 3176)
  covalent geometry    : angle       0.56919 ( 4340)
  hydrogen bonds       : bond        0.03869 (  231)
  hydrogen bonds       : angle       3.95050 (  693)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A   20 CYS cc_start: 0.5793 (t) cc_final: 0.5064 (m)
REVERT: A   97 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6696 (mp)
REVERT: A  305 TYR cc_start: 0.6184 (m-10) cc_final: 0.5927 (t80)
  outliers start: 8
  outliers final: 7
  residues processed: 45
  average time/residue: 0.0341
  time to fit residues: 2.1999
Evaluate side-chains
  48 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  140 SER
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  421 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 18 optimal weight:    0.1980
   chunk 36 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    0.2980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.4298 r_free = 0.4298 target = 0.209830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.185424 restraints weight = 3295.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.4080 rms_B_bonded: 1.56
r_work: 0.3986 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3857 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6688
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3176  Z= 0.128
  Angle     :  0.534   5.488   4340  Z= 0.270
  Chirality :  0.040   0.150    498
  Planarity :  0.004   0.037    516
  Dihedral  : 10.063 135.837    434
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.21 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.44), residues: 378
  helix:  1.42 (0.30), residues: 306
  sheet:  None (None), residues: 0
  loop : -0.45 (0.80), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  78 
 TYR   0.013   0.001   TYR A  79 
 PHE   0.007   0.001   PHE A 279 
 TRP   0.016   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3176)
  covalent geometry    : angle       0.53432 ( 4340)
  hydrogen bonds       : bond        0.03602 (  231)
  hydrogen bonds       : angle       3.85035 (  693)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A   20 CYS cc_start: 0.5777 (t) cc_final: 0.5067 (m)
REVERT: A   97 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6645 (mp)
REVERT: A  305 TYR cc_start: 0.6226 (m-10) cc_final: 0.5934 (t80)
  outliers start: 8
  outliers final: 6
  residues processed: 45
  average time/residue: 0.0362
  time to fit residues: 2.3512
Evaluate side-chains
  46 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  421 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 16 optimal weight:    0.3980
   chunk 32 optimal weight:    0.6980
   chunk 37 optimal weight:    0.1980
   chunk 23 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4315 r_free = 0.4315 target = 0.210392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.186320 restraints weight = 3236.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.4078 rms_B_bonded: 1.54
r_work: 0.3984 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3856 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6699
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3176  Z= 0.137
  Angle     :  0.553   6.070   4340  Z= 0.279
  Chirality :  0.040   0.151    498
  Planarity :  0.004   0.037    516
  Dihedral  : 10.048 135.281    434
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.51 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.44), residues: 378
  helix:  1.40 (0.30), residues: 307
  sheet:  None (None), residues: 0
  loop : -0.31 (0.80), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  78 
 TYR   0.013   0.001   TYR A  79 
 PHE   0.008   0.001   PHE A 189 
 TRP   0.014   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3176)
  covalent geometry    : angle       0.55316 ( 4340)
  hydrogen bonds       : bond        0.03701 (  231)
  hydrogen bonds       : angle       3.88105 (  693)

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

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

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  756 Ramachandran restraints generated.
    378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A   20 CYS cc_start: 0.5793 (t) cc_final: 0.5071 (m)
REVERT: A   97 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6667 (mp)
REVERT: A  305 TYR cc_start: 0.6210 (m-10) cc_final: 0.5929 (t80)
  outliers start: 8
  outliers final: 7
  residues processed: 44
  average time/residue: 0.0375
  time to fit residues: 2.3917
Evaluate side-chains
  47 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  140 SER
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  421 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 25 optimal weight:    0.3980
   chunk 21 optimal weight:    0.6980
   chunk 29 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.4296 r_free = 0.4296 target = 0.209216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.184815 restraints weight = 3281.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.4108 rms_B_bonded: 1.55
r_work: 0.4013 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3885 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6699
moved from start:          0.1753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3176  Z= 0.137
  Angle     :  0.552   5.830   4340  Z= 0.278
  Chirality :  0.040   0.150    498
  Planarity :  0.004   0.037    516
  Dihedral  : 10.050 135.150    434
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.43 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.44), residues: 378
  helix:  1.41 (0.30), residues: 307
  sheet:  None (None), residues: 0
  loop : -0.30 (0.81), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  78 
 TYR   0.013   0.001   TYR A  79 
 PHE   0.007   0.001   PHE A  22 
 TRP   0.014   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3176)
  covalent geometry    : angle       0.55215 ( 4340)
  hydrogen bonds       : bond        0.03696 (  231)
  hydrogen bonds       : angle       3.88482 (  693)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1018.72 seconds
wall clock time: 18 minutes 9.98 seconds (1089.98 seconds total)