Starting phenix.real_space_refine
on Wed Jun  4 13:42:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qcs_18334/06_2025/8qcs_18334.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qcs_18334/06_2025/8qcs_18334.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qcs_18334/06_2025/8qcs_18334.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qcs_18334/06_2025/8qcs_18334.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qcs_18334/06_2025/8qcs_18334.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qcs_18334/06_2025/8qcs_18334.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.003 sd=   0.097
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      18      5.16       5
     C    2156      2.51       5
     N     500      2.21       5
     O     567      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3241
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 417, 3241
          Classifications: {'peptide': 417}
          Link IDs: {'PTRANS': 17, 'TRANS': 399}
  Time building chain proxies: 2.69, per 1000 atoms: 0.83
  Number of scatterers: 3241
  At special positions: 0
  Unit cell: (80.22, 55.008, 65.322, 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      18     16.00
     O     567      8.00
     N     500      7.00
     C    2156      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: 0.83
  Conformation dependent library (CDL) restraints added in 433.4 milliseconds
  

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  764

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 0 sheets defined
      90.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 105 through 127
      removed outlier: 4.213A  pdb=" N   VAL A 109 " --> pdb=" O   PRO A 105 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ILE A 126 " --> pdb=" O   ALA A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 140
      removed outlier: 4.068A  pdb=" N   GLY A 137 " --> pdb=" O   ASN A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 156
      removed outlier: 3.719A  pdb=" N   ILE A 146 " --> pdb=" O   THR A 142 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   SER A 150 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   TYR A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   MET A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 171
      removed outlier: 3.722A  pdb=" N   LEU A 160 " --> pdb=" O   ALA A 156 " (cutoff:3.500A)
      removed outlier: 5.203A  pdb=" N   PHE A 162 " --> pdb=" O   VAL A 158 " (cutoff:3.500A)
      Proline residue:  A 163  - end of helix
    Processing helix  chain 'A' and resid 172 through 193
      removed outlier: 3.712A  pdb=" N   THR A 176 " --> pdb=" O   GLY A 172 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLY A 193 " --> pdb=" O   TRP A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 219
      removed outlier: 3.555A  pdb=" N   THR A 203 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   VAL A 215 " --> pdb=" O   SER A 211 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   PHE A 216 " --> pdb=" O   VAL A 212 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   GLY A 219 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 229
      removed outlier: 4.349A  pdb=" N   ARG A 223 " --> pdb=" O   GLY A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 232
      No H-bonds generated for 'chain 'A' and resid 230 through 232'
    Processing helix  chain 'A' and resid 233 through 260
      removed outlier: 3.502A  pdb=" N   THR A 249 " --> pdb=" O   ASN A 245 " (cutoff:3.500A)
      Proline residue:  A 256  - end of helix
    Processing helix  chain 'A' and resid 266 through 296
    Processing helix  chain 'A' and resid 305 through 313
      removed outlier: 3.777A  pdb=" N   ASP A 313 " --> pdb=" O   ALA A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 319
      removed outlier: 6.226A  pdb=" N   GLU A 317 " --> pdb=" O   SER A 314 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   GLU A 318 " --> pdb=" O   PRO A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 329
      removed outlier: 3.542A  pdb=" N   PHE A 329 " --> pdb=" O   ILE A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 363
      removed outlier: 3.709A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   ASN A 356 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
      removed outlier: 5.632A  pdb=" N   GLN A 357 " --> pdb=" O   THR A 353 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   THR A 361 " --> pdb=" O   GLN A 357 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   TYR A 362 " --> pdb=" O   MET A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 393
      removed outlier: 4.112A  pdb=" N   GLY A 381 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   ASP A 393 " --> pdb=" O   GLY A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 418
      removed outlier: 3.518A  pdb=" N   MET A 413 " --> pdb=" O   SER A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 423
    Processing helix  chain 'A' and resid 424 through 440
      removed outlier: 3.721A  pdb=" N   VAL A 428 " --> pdb=" O   TYR A 424 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   PHE A 438 " --> pdb=" O   VAL A 434 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   THR A 440 " --> pdb=" O   GLY A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 453
    Processing helix  chain 'A' and resid 458 through 489
      removed outlier: 3.768A  pdb=" N   SER A 462 " --> pdb=" O   SER A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 511
      removed outlier: 3.556A  pdb=" N   LEU A 497 " --> pdb=" O   GLY A 493 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ILE A 511 " --> pdb=" O   LEU A 507 " (cutoff:3.500A)

    255 hydrogen bonds defined for protein.
    756 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: 0.92

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 961
        1.34 -     1.46: 641
        1.46 -     1.57: 1693
        1.57 -     1.69: 0
        1.69 -     1.81: 28
  Bond restraints: 3323
  Sorted by residual:
  bond pdb=" N   ILE A 427 "
       pdb=" CA  ILE A 427 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.30e-02 5.92e+03 7.52e+00
  bond pdb=" N   GLN A 308 "
       pdb=" CA  GLN A 308 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.30e-02 5.92e+03 5.28e+00
  bond pdb=" N   ASP A 169 "
       pdb=" CA  ASP A 169 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.030 1.33e-02 5.65e+03 4.95e+00
  bond pdb=" CB  GLN A 306 "
       pdb=" CG  GLN A 306 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.82e-01
  bond pdb=" C   ILE A 427 "
       pdb=" N   VAL A 428 "
    ideal  model  delta    sigma   weight residual
    1.335  1.324  0.011 1.20e-02 6.94e+03 8.92e-01
  ... (remaining 3318 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 4444
        1.69 -     3.39: 66
        3.39 -     5.08: 16
        5.08 -     6.77: 7
        6.77 -     8.47: 1
  Bond angle restraints: 4534
  Sorted by residual:
  angle pdb=" C   ALA A 307 "
        pdb=" N   GLN A 308 "
        pdb=" CA  GLN A 308 "
      ideal   model   delta    sigma   weight residual
     120.68  115.80    4.88 1.70e+00 3.46e-01 8.23e+00
  angle pdb=" N   GLN A 308 "
        pdb=" CA  GLN A 308 "
        pdb=" C   GLN A 308 "
      ideal   model   delta    sigma   weight residual
     112.23  108.88    3.35 1.26e+00 6.30e-01 7.09e+00
  angle pdb=" N   LEU A 220 "
        pdb=" CA  LEU A 220 "
        pdb=" C   LEU A 220 "
      ideal   model   delta    sigma   weight residual
     109.81  115.56   -5.75 2.21e+00 2.05e-01 6.76e+00
  angle pdb=" N   LYS A 396 "
        pdb=" CA  LYS A 396 "
        pdb=" C   LYS A 396 "
      ideal   model   delta    sigma   weight residual
     108.34  111.55   -3.21 1.31e+00 5.83e-01 6.02e+00
  angle pdb=" CA  LEU A 269 "
        pdb=" CB  LEU A 269 "
        pdb=" CG  LEU A 269 "
      ideal   model   delta    sigma   weight residual
     116.30  124.77   -8.47 3.50e+00 8.16e-02 5.85e+00
  ... (remaining 4529 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 1697
       17.51 -    35.02: 168
       35.02 -    52.53: 34
       52.53 -    70.05: 13
       70.05 -    87.56: 2
  Dihedral angle restraints: 1914
    sinusoidal: 714
      harmonic: 1200
  Sorted by residual:
  dihedral pdb=" CA  ASP A 421 "
           pdb=" CB  ASP A 421 "
           pdb=" CG  ASP A 421 "
           pdb=" OD1 ASP A 421 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.73   56.73     1      2.00e+01 2.50e-03 1.08e+01
  dihedral pdb=" CA  TYR A 117 "
           pdb=" C   TYR A 117 "
           pdb=" N   SER A 118 "
           pdb=" CA  SER A 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.76   16.24     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" CA  THR A 440 "
           pdb=" C   THR A 440 "
           pdb=" N   GLY A 441 "
           pdb=" CA  GLY A 441 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.17   15.83     0      5.00e+00 4.00e-02 1.00e+01
  ... (remaining 1911 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 316
       0.026 -    0.051: 130
       0.051 -    0.077: 66
       0.077 -    0.102: 23
       0.102 -    0.128: 8
  Chirality restraints: 543
  Sorted by residual:
  chirality pdb=" CA  ILE A 427 "
            pdb=" N   ILE A 427 "
            pdb=" C   ILE A 427 "
            pdb=" CB  ILE A 427 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.07e-01
  chirality pdb=" CA  PRO A 221 "
            pdb=" N   PRO A 221 "
            pdb=" C   PRO A 221 "
            pdb=" CB  PRO A 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 3.15e-01
  chirality pdb=" CA  TYR A 117 "
            pdb=" N   TYR A 117 "
            pdb=" C   TYR A 117 "
            pdb=" CB  TYR A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 3.02e-01
  ... (remaining 540 not shown)

  Planarity restraints: 550
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 443 "   -0.022 5.00e-02 4.00e+02   3.35e-02 1.80e+00
        pdb=" N   PRO A 444 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 444 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 444 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 255 "   -0.020 5.00e-02 4.00e+02   2.94e-02 1.38e+00
        pdb=" N   PRO A 256 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO A 256 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 256 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 256 "    0.018 5.00e-02 4.00e+02   2.64e-02 1.11e+00
        pdb=" N   PRO A 257 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO A 257 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 257 "    0.015 5.00e-02 4.00e+02
  ... (remaining 547 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1003
        2.82 -     3.34: 3277
        3.34 -     3.86: 5409
        3.86 -     4.38: 6478
        4.38 -     4.90: 10937
  Nonbonded interactions: 27104
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 262 "
            pdb=" OE1 GLU A 367 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" O   ILE A 415 "
            pdb=" OG1 THR A 419 "
     model   vdw
     2.380 3.040
  nonbonded pdb=" OH  TYR A 319 "
            pdb=" OG  SER A 458 "
     model   vdw
     2.383 3.040
  nonbonded pdb=" O   GLY A 504 "
            pdb=" OG1 THR A 508 "
     model   vdw
     2.419 3.040
  nonbonded pdb=" NE1 TRP A 189 "
            pdb=" OG1 THR A 286 "
     model   vdw
     2.424 3.120
  ... (remaining 27099 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:             0.340
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.620
  Find NCS groups from input model:        0.030
  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:16.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
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      :  0.003   0.036   3323  Z= 0.136
  Angle     :  0.571   8.467   4534  Z= 0.294
  Chirality :  0.038   0.128    543
  Planarity :  0.003   0.034    550
  Dihedral  : 15.225  87.558   1150
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.11 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.39), residues: 415
  helix:  0.91 (0.28), residues: 324
  sheet:  None (None), residues: 0
  loop : -1.18 (0.58), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 500 
 HIS   0.001   0.001   HIS A 145 
 PHE   0.008   0.001   PHE A 162 
 TYR   0.016   0.001   TYR A 117 
 ARG   0.001   0.000   ARG A 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24584 (  255)
  hydrogen bonds       : angle       7.70171 (  756)
  covalent geometry    : bond        0.00285 ( 3323)
  covalent geometry    : angle       0.57116 ( 4534)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.365 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 1.2786
  time to fit residues: 52.7438
Evaluate side-chains
  37 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0010
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 369 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.135398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.107385 restraints weight = 4006.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 2.15
r_work: 0.3042 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3323  Z= 0.144
  Angle     :  0.610   7.432   4534  Z= 0.312
  Chirality :  0.040   0.152    543
  Planarity :  0.004   0.031    550
  Dihedral  :  4.104  15.377    446
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 18.70 %
    Favored  : 79.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.41), residues: 415
  helix:  1.69 (0.28), residues: 335
  sheet:  None (None), residues: 0
  loop : -1.61 (0.58), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 500 
 HIS   0.001   0.000   HIS A 198 
 PHE   0.010   0.001   PHE A 496 
 TYR   0.024   0.001   TYR A 117 
 ARG   0.001   0.000   ARG A 107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05414 (  255)
  hydrogen bonds       : angle       4.90299 (  756)
  covalent geometry    : bond        0.00300 ( 3323)
  covalent geometry    : angle       0.60994 ( 4534)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A  136 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6479 (mt-10)
REVERT: A  169 ASP cc_start: 0.7570 (m-30) cc_final: 0.7186 (m-30)
REVERT: A  390 LEU cc_start: 0.7428 (mt) cc_final: 0.6649 (tt)
REVERT: A  409 SER cc_start: 0.9003 (t) cc_final: 0.8751 (m)
  outliers start: 6
  outliers final: 1
  residues processed: 53
  average time/residue: 1.0957
  time to fit residues: 60.0264
Evaluate side-chains
  43 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  440 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   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 = 0.3549 r_free = 0.3549 target = 0.134567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.105911 restraints weight = 4060.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 2.17
r_work: 0.3024 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3323  Z= 0.141
  Angle     :  0.589   8.795   4534  Z= 0.298
  Chirality :  0.040   0.149    543
  Planarity :  0.004   0.030    550
  Dihedral  :  4.023  14.839    446
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.41 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.41), residues: 415
  helix:  1.89 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.88 (0.58), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 500 
 HIS   0.001   0.001   HIS A 145 
 PHE   0.011   0.001   PHE A 496 
 TYR   0.025   0.001   TYR A 117 
 ARG   0.005   0.000   ARG A 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04698 (  255)
  hydrogen bonds       : angle       4.57964 (  756)
  covalent geometry    : bond        0.00305 ( 3323)
  covalent geometry    : angle       0.58892 ( 4534)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A  136 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6327 (mt-10)
REVERT: A  390 LEU cc_start: 0.7569 (mt) cc_final: 0.6795 (tt)
  outliers start: 11
  outliers final: 2
  residues processed: 52
  average time/residue: 1.1336
  time to fit residues: 61.0353
Evaluate side-chains
  43 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 40
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  413 MET
Chi-restraints excluded: chain A residue  440 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   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 = 0.3551 r_free = 0.3551 target = 0.134626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.105949 restraints weight = 4138.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 2.21
r_work: 0.3065 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3323  Z= 0.135
  Angle     :  0.582   7.042   4534  Z= 0.294
  Chirality :  0.039   0.151    543
  Planarity :  0.004   0.030    550
  Dihedral  :  4.053  15.305    446
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 19.26 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.41), residues: 415
  helix:  2.08 (0.29), residues: 326
  sheet:  None (None), residues: 0
  loop : -1.85 (0.55), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 500 
 HIS   0.001   0.000   HIS A 145 
 PHE   0.010   0.001   PHE A 496 
 TYR   0.025   0.001   TYR A 117 
 ARG   0.004   0.000   ARG A 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04325 (  255)
  hydrogen bonds       : angle       4.41320 (  756)
  covalent geometry    : bond        0.00295 ( 3323)
  covalent geometry    : angle       0.58247 ( 4534)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A  126 ILE cc_start: 0.8862 (tp) cc_final: 0.8556 (tp)
REVERT: A  136 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6316 (mt-10)
REVERT: A  388 CYS cc_start: 0.6718 (OUTLIER) cc_final: 0.5549 (m)
REVERT: A  390 LEU cc_start: 0.7465 (mt) cc_final: 0.6608 (tt)
  outliers start: 11
  outliers final: 2
  residues processed: 50
  average time/residue: 1.2562
  time to fit residues: 64.7610
Evaluate side-chains
  44 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain A residue  440 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0570
   chunk 3 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.5498

-------------------------------------------------------------------------------
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 = 0.3564 r_free = 0.3564 target = 0.135853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.107322 restraints weight = 4121.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 2.14
r_work: 0.3061 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3323  Z= 0.125
  Angle     :  0.573   7.349   4534  Z= 0.288
  Chirality :  0.039   0.149    543
  Planarity :  0.004   0.030    550
  Dihedral  :  4.024  15.852    446
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 19.26 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.42), residues: 415
  helix:  2.15 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.76 (0.57), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 500 
 HIS   0.001   0.000   HIS A 145 
 PHE   0.010   0.001   PHE A 496 
 TYR   0.024   0.001   TYR A 117 
 ARG   0.005   0.000   ARG A 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04145 (  255)
  hydrogen bonds       : angle       4.26592 (  756)
  covalent geometry    : bond        0.00264 ( 3323)
  covalent geometry    : angle       0.57338 ( 4534)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.328 
Fit side-chains
REVERT: A  126 ILE cc_start: 0.8849 (tp) cc_final: 0.8565 (tp)
REVERT: A  136 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6339 (mt-10)
REVERT: A  388 CYS cc_start: 0.6611 (OUTLIER) cc_final: 0.5477 (m)
REVERT: A  390 LEU cc_start: 0.7454 (mt) cc_final: 0.6652 (tt)
  outliers start: 15
  outliers final: 3
  residues processed: 54
  average time/residue: 1.0833
  time to fit residues: 60.4425
Evaluate side-chains
  46 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain A residue  440 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3535 r_free = 0.3535 target = 0.133215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.104426 restraints weight = 4218.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 2.22
r_work: 0.3015 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3323  Z= 0.149
  Angle     :  0.597   7.092   4534  Z= 0.300
  Chirality :  0.040   0.157    543
  Planarity :  0.004   0.032    550
  Dihedral  :  4.100  16.399    446
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 21.25 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.42), residues: 415
  helix:  2.15 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.67 (0.58), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 500 
 HIS   0.002   0.001   HIS A 145 
 PHE   0.011   0.001   PHE A 334 
 TYR   0.025   0.001   TYR A 117 
 ARG   0.007   0.001   ARG A 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04293 (  255)
  hydrogen bonds       : angle       4.27680 (  756)
  covalent geometry    : bond        0.00344 ( 3323)
  covalent geometry    : angle       0.59676 ( 4534)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A  136 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6614 (mt-10)
REVERT: A  388 CYS cc_start: 0.6347 (OUTLIER) cc_final: 0.5510 (m)
REVERT: A  390 LEU cc_start: 0.7529 (mt) cc_final: 0.6736 (tt)
REVERT: A  445 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8179 (mm)
  outliers start: 12
  outliers final: 4
  residues processed: 52
  average time/residue: 1.1287
  time to fit residues: 60.6141
Evaluate side-chains
  47 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  445 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3540 r_free = 0.3540 target = 0.133771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.105342 restraints weight = 4139.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 2.13
r_work: 0.3098 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3323  Z= 0.135
  Angle     :  0.591   8.181   4534  Z= 0.296
  Chirality :  0.040   0.154    543
  Planarity :  0.004   0.030    550
  Dihedral  :  4.078  16.422    446
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 21.53 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.25 (0.42), residues: 415
  helix:  2.22 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.68 (0.57), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 500 
 HIS   0.001   0.001   HIS A 145 
 PHE   0.010   0.001   PHE A 496 
 TYR   0.024   0.001   TYR A 117 
 ARG   0.007   0.001   ARG A 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04131 (  255)
  hydrogen bonds       : angle       4.22646 (  756)
  covalent geometry    : bond        0.00303 ( 3323)
  covalent geometry    : angle       0.59137 ( 4534)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.455 
Fit side-chains
REVERT: A  126 ILE cc_start: 0.8880 (tp) cc_final: 0.8549 (tp)
REVERT: A  136 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6339 (mt-10)
REVERT: A  323 LYS cc_start: 0.7829 (tmtp) cc_final: 0.7274 (tmmt)
REVERT: A  388 CYS cc_start: 0.6326 (OUTLIER) cc_final: 0.5514 (m)
REVERT: A  390 LEU cc_start: 0.7393 (mt) cc_final: 0.6612 (tt)
REVERT: A  445 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7967 (mm)
  outliers start: 12
  outliers final: 4
  residues processed: 53
  average time/residue: 1.0464
  time to fit residues: 57.4998
Evaluate side-chains
  47 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  445 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0470
   chunk 15 optimal weight:    0.0470
   chunk 4 optimal weight:    0.0870
   chunk 38 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.3354

-------------------------------------------------------------------------------
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 = 0.3583 r_free = 0.3583 target = 0.137737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.108773 restraints weight = 4174.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 2.28
r_work: 0.3038 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3323  Z= 0.117
  Angle     :  0.569   7.619   4534  Z= 0.284
  Chirality :  0.038   0.149    543
  Planarity :  0.004   0.030    550
  Dihedral  :  3.953  15.640    446
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 22.10 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.42), residues: 415
  helix:  2.29 (0.29), residues: 334
  sheet:  None (None), residues: 0
  loop : -1.69 (0.58), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 500 
 HIS   0.000   0.000   HIS A 198 
 PHE   0.011   0.001   PHE A 496 
 TYR   0.024   0.001   TYR A 117 
 ARG   0.006   0.001   ARG A 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03765 (  255)
  hydrogen bonds       : angle       4.08605 (  756)
  covalent geometry    : bond        0.00240 ( 3323)
  covalent geometry    : angle       0.56896 ( 4534)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A  126 ILE cc_start: 0.8695 (tp) cc_final: 0.8432 (tp)
REVERT: A  136 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6166 (mt-10)
REVERT: A  147 ASP cc_start: 0.7938 (m-30) cc_final: 0.7700 (m-30)
REVERT: A  174 ARG cc_start: 0.7831 (ttt90) cc_final: 0.7572 (ttm-80)
REVERT: A  279 TYR cc_start: 0.6601 (t80) cc_final: 0.5454 (m-80)
REVERT: A  388 CYS cc_start: 0.6337 (OUTLIER) cc_final: 0.5628 (m)
REVERT: A  390 LEU cc_start: 0.7339 (mt) cc_final: 0.6587 (tt)
REVERT: A  445 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7841 (mm)
  outliers start: 11
  outliers final: 5
  residues processed: 50
  average time/residue: 1.1240
  time to fit residues: 58.0538
Evaluate side-chains
  49 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  275 SER
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  445 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 4 optimal weight:    0.3980
   chunk 35 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 15 optimal weight:    0.4980
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3553 r_free = 0.3553 target = 0.134959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.106566 restraints weight = 4221.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 2.18
r_work: 0.2978 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2863 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3323  Z= 0.139
  Angle     :  0.593   8.789   4534  Z= 0.295
  Chirality :  0.040   0.156    543
  Planarity :  0.004   0.030    550
  Dihedral  :  4.016  15.742    446
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 22.66 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.42), residues: 415
  helix:  2.25 (0.29), residues: 335
  sheet:  None (None), residues: 0
  loop : -1.56 (0.58), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 500 
 HIS   0.001   0.000   HIS A 145 
 PHE   0.010   0.001   PHE A 496 
 TYR   0.025   0.001   TYR A 117 
 ARG   0.007   0.001   ARG A 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04008 (  255)
  hydrogen bonds       : angle       4.13441 (  756)
  covalent geometry    : bond        0.00319 ( 3323)
  covalent geometry    : angle       0.59319 ( 4534)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A  126 ILE cc_start: 0.8782 (tp) cc_final: 0.8504 (tp)
REVERT: A  136 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6334 (mt-10)
REVERT: A  147 ASP cc_start: 0.8065 (m-30) cc_final: 0.7849 (m-30)
REVERT: A  174 ARG cc_start: 0.7924 (ttt90) cc_final: 0.7631 (ttm-80)
REVERT: A  279 TYR cc_start: 0.6721 (t80) cc_final: 0.5541 (m-80)
REVERT: A  323 LYS cc_start: 0.7680 (tmtp) cc_final: 0.7130 (tmmt)
REVERT: A  388 CYS cc_start: 0.6219 (OUTLIER) cc_final: 0.5509 (m)
REVERT: A  390 LEU cc_start: 0.7351 (mt) cc_final: 0.6593 (tt)
REVERT: A  445 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7903 (mm)
  outliers start: 9
  outliers final: 5
  residues processed: 52
  average time/residue: 1.1721
  time to fit residues: 62.8543
Evaluate side-chains
  47 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  445 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0470
   chunk 1 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0050
   chunk 38 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0970
   chunk 28 optimal weight:    0.9980
   chunk 29 optimal weight:    8.9990
   overall best weight:    0.3090

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.138868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.111011 restraints weight = 4106.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 2.14
r_work: 0.3104 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.2656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   3323  Z= 0.117
  Angle     :  0.576   8.787   4534  Z= 0.286
  Chirality :  0.038   0.148    543
  Planarity :  0.004   0.029    550
  Dihedral  :  3.898  15.635    446
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 22.10 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.42), residues: 415
  helix:  2.37 (0.29), residues: 334
  sheet:  None (None), residues: 0
  loop : -1.59 (0.59), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 500 
 HIS   0.000   0.000   HIS A 145 
 PHE   0.011   0.001   PHE A 496 
 TYR   0.024   0.001   TYR A 117 
 ARG   0.007   0.001   ARG A 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03721 (  255)
  hydrogen bonds       : angle       4.03380 (  756)
  covalent geometry    : bond        0.00240 ( 3323)
  covalent geometry    : angle       0.57593 ( 4534)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A  126 ILE cc_start: 0.8891 (tp) cc_final: 0.8630 (tp)
REVERT: A  136 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6355 (mt-10)
REVERT: A  147 ASP cc_start: 0.8158 (m-30) cc_final: 0.7923 (m-30)
REVERT: A  174 ARG cc_start: 0.8143 (ttt90) cc_final: 0.7879 (ttm-80)
REVERT: A  279 TYR cc_start: 0.6874 (t80) cc_final: 0.5689 (m-80)
REVERT: A  388 CYS cc_start: 0.6342 (OUTLIER) cc_final: 0.5728 (m)
REVERT: A  445 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8107 (mm)
  outliers start: 11
  outliers final: 4
  residues processed: 51
  average time/residue: 1.1096
  time to fit residues: 58.5274
Evaluate side-chains
  45 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  388 CYS
Chi-restraints excluded: chain A residue  409 SER
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  445 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 12 optimal weight:    0.3980
   chunk 18 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3566 r_free = 0.3566 target = 0.136156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.108051 restraints weight = 4167.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 2.16
r_work: 0.3038 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3323  Z= 0.127
  Angle     :  0.576   8.700   4534  Z= 0.289
  Chirality :  0.039   0.153    543
  Planarity :  0.004   0.030    550
  Dihedral  :  3.918  15.770    446
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 23.80 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.42), residues: 415
  helix:  2.32 (0.29), residues: 335
  sheet:  None (None), residues: 0
  loop : -1.50 (0.59), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 500 
 HIS   0.000   0.000   HIS A 198 
 PHE   0.010   0.001   PHE A 496 
 TYR   0.024   0.001   TYR A 117 
 ARG   0.007   0.001   ARG A 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03861 (  255)
  hydrogen bonds       : angle       4.07109 (  756)
  covalent geometry    : bond        0.00284 ( 3323)
  covalent geometry    : angle       0.57604 ( 4534)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2530.23 seconds
wall clock time: 44 minutes 0.13 seconds (2640.13 seconds total)