Starting phenix.real_space_refine
on Wed Mar  5 17:19:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wyk_21967/03_2025/6wyk_21967.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wyk_21967/03_2025/6wyk_21967.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wyk_21967/03_2025/6wyk_21967.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wyk_21967/03_2025/6wyk_21967.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wyk_21967/03_2025/6wyk_21967.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wyk_21967/03_2025/6wyk_21967.cif"
  }
  resolution = 4.0
  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=   0.000 sd=   0.003
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    2029      2.51       5
     N     490      2.21       5
     O     546      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3083
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3083
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3083
          Classifications: {'peptide': 415}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 396}
          Chain breaks: 1
  Time building chain proxies: 2.59, per 1000 atoms: 0.84
  Number of scatterers: 3083
  At special positions: 0
  Unit cell: (73.95, 70.992, 76.908, 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     546      8.00
     N     490      7.00
     C    2029      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: 0.94
  Conformation dependent library (CDL) restraints added in 373.0 milliseconds
  

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  750

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      86.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 10
    Processing helix  chain 'A' and resid 13 through 29
      removed outlier: 4.045A  pdb=" N   LEU A  17 " --> pdb=" O   LEU A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 78
      Proline residue:  A  45  - end of helix
      removed outlier: 3.508A  pdb=" N   PHE A  50 " --> pdb=" O   PHE A  46 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LEU A  57 " --> pdb=" O   LEU A  53 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   VAL A  58 " --> pdb=" O   LEU A  54 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   MET A  59 " --> pdb=" O   LYS A  55 " (cutoff:3.500A)
      Proline residue:  A  60  - end of helix
      removed outlier: 3.530A  pdb=" N   PHE A  63 " --> pdb=" O   MET A  59 " (cutoff:3.500A)
      Proline residue:  A  75  - end of helix
    Processing helix  chain 'A' and resid 79 through 108
    Processing helix  chain 'A' and resid 129 through 137
      removed outlier: 3.510A  pdb=" N   ILE A 133 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ILE A 137 " --> pdb=" O   ILE A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 149
      removed outlier: 3.671A  pdb=" N   GLY A 149 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 170
      removed outlier: 4.268A  pdb=" N   ASN A 170 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 221
      removed outlier: 4.025A  pdb=" N   GLN A 203 " --> pdb=" O   ASN A 199 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   TYR A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
      Proline residue:  A 206  - end of helix
      removed outlier: 3.780A  pdb=" N   GLN A 220 " --> pdb=" O   VAL A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 255
      removed outlier: 3.832A  pdb=" N   GLU A 227 " --> pdb=" O   LYS A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 276
      removed outlier: 4.420A  pdb=" N   ASP A 267 " --> pdb=" O   LYS A 263 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   ALA A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   THR A 271 " --> pdb=" O   ASP A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 293
      removed outlier: 4.021A  pdb=" N   VAL A 284 " --> pdb=" O   GLY A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      Proline residue:  A 304  - end of helix
    Processing helix  chain 'A' and resid 312 through 330
    Processing helix  chain 'A' and resid 334 through 352
    Processing helix  chain 'A' and resid 357 through 370
      removed outlier: 4.388A  pdb=" N   ILE A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   MET A 362 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   LEU A 363 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   MET A 365 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 416
      removed outlier: 3.667A  pdb=" N   GLY A 388 " --> pdb=" O   ALA A 384 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   ILE A 389 " --> pdb=" O   MET A 385 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ALA A 391 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   ILE A 392 " --> pdb=" O   GLY A 388 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   MET A 395 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLY A 396 " --> pdb=" O   ILE A 392 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   MET A 399 " --> pdb=" O   MET A 395 " (cutoff:3.500A)

    251 hydrogen bonds defined for protein.
    753 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: 0.79

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 946
        1.34 -     1.46: 451
        1.46 -     1.57: 1705
        1.57 -     1.69: 0
        1.69 -     1.81: 34
  Bond restraints: 3136
  Sorted by residual:
  bond pdb=" N   VAL A 225 "
       pdb=" CA  VAL A 225 "
    ideal  model  delta    sigma   weight residual
    1.459  1.507 -0.048 1.33e-02 5.65e+03 1.29e+01
  bond pdb=" N   VAL A 274 "
       pdb=" CA  VAL A 274 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.037 1.21e-02 6.83e+03 9.53e+00
  bond pdb=" N   LYS A 223 "
       pdb=" CA  LYS A 223 "
    ideal  model  delta    sigma   weight residual
    1.456  1.496 -0.040 1.31e-02 5.83e+03 9.29e+00
  bond pdb=" N   VAL A 224 "
       pdb=" CA  VAL A 224 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.036 1.26e-02 6.30e+03 8.36e+00
  bond pdb=" N   ASN A 148 "
       pdb=" CA  ASN A 148 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.29e-02 6.01e+03 7.37e+00
  ... (remaining 3131 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.12: 3886
        1.12 -     2.24: 289
        2.24 -     3.36: 55
        3.36 -     4.48: 32
        4.48 -     5.59: 7
  Bond angle restraints: 4269
  Sorted by residual:
  angle pdb=" CA  VAL A 224 "
        pdb=" C   VAL A 224 "
        pdb=" O   VAL A 224 "
      ideal   model   delta    sigma   weight residual
     120.57  115.75    4.82 1.07e+00 8.73e-01 2.03e+01
  angle pdb=" CA  GLN A 150 "
        pdb=" C   GLN A 150 "
        pdb=" O   GLN A 150 "
      ideal   model   delta    sigma   weight residual
     120.32  115.83    4.49 1.11e+00 8.12e-01 1.64e+01
  angle pdb=" CA  VAL A 274 "
        pdb=" C   VAL A 274 "
        pdb=" O   VAL A 274 "
      ideal   model   delta    sigma   weight residual
     120.85  116.85    4.00 1.06e+00 8.90e-01 1.43e+01
  angle pdb=" CA  THR A 275 "
        pdb=" C   THR A 275 "
        pdb=" O   THR A 275 "
      ideal   model   delta    sigma   weight residual
     119.97  115.76    4.21 1.15e+00 7.56e-01 1.34e+01
  angle pdb=" CA  PHE A 273 "
        pdb=" C   PHE A 273 "
        pdb=" O   PHE A 273 "
      ideal   model   delta    sigma   weight residual
     120.82  117.24    3.58 1.05e+00 9.07e-01 1.16e+01
  ... (remaining 4264 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.92: 1699
       15.92 -    31.83: 138
       31.83 -    47.75: 26
       47.75 -    63.66: 2
       63.66 -    79.58: 1
  Dihedral angle restraints: 1866
    sinusoidal: 685
      harmonic: 1181
  Sorted by residual:
  dihedral pdb=" CA  ILE A  73 "
           pdb=" C   ILE A  73 "
           pdb=" N   SER A  74 "
           pdb=" CA  SER A  74 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.13  -25.87     0      5.00e+00 4.00e-02 2.68e+01
  dihedral pdb=" CA  PRO A 109 "
           pdb=" C   PRO A 109 "
           pdb=" N   GLY A 110 "
           pdb=" CA  GLY A 110 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.97  -25.03     0      5.00e+00 4.00e-02 2.51e+01
  dihedral pdb=" CA  GLY A 221 "
           pdb=" C   GLY A 221 "
           pdb=" N   VAL A 222 "
           pdb=" CA  VAL A 222 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.02  -20.98     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 1863 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 411
       0.053 -    0.106: 109
       0.106 -    0.159: 13
       0.159 -    0.212: 3
       0.212 -    0.266: 2
  Chirality restraints: 538
  Sorted by residual:
  chirality pdb=" CB  VAL A 224 "
            pdb=" CA  VAL A 224 "
            pdb=" CG1 VAL A 224 "
            pdb=" CG2 VAL A 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CB  VAL A 225 "
            pdb=" CA  VAL A 225 "
            pdb=" CG1 VAL A 225 "
            pdb=" CG2 VAL A 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  GLN A 150 "
            pdb=" N   GLN A 150 "
            pdb=" C   GLN A 150 "
            pdb=" CB  GLN A 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.45e-01
  ... (remaining 535 not shown)

  Planarity restraints: 524
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 147 "    0.015 2.00e-02 2.50e+03   2.87e-02 8.23e+00
        pdb=" C   ALA A 147 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   ALA A 147 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ASN A 148 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 299 "    0.022 2.00e-02 2.50e+03   1.80e-02 6.46e+00
        pdb=" CG  TYR A 299 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 299 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 299 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 299 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 299 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 299 "    0.008 2.00e-02 2.50e+03
        pdb=" OH  TYR A 299 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 224 "    0.010 2.00e-02 2.50e+03   2.06e-02 4.25e+00
        pdb=" C   VAL A 224 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   VAL A 224 "    0.013 2.00e-02 2.50e+03
        pdb=" N   VAL A 225 "    0.013 2.00e-02 2.50e+03
  ... (remaining 521 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 560
        2.76 -     3.29: 3550
        3.29 -     3.83: 4990
        3.83 -     4.36: 5548
        4.36 -     4.90: 9361
  Nonbonded interactions: 24009
  Sorted by model distance:
  nonbonded pdb=" O   ALA A  71 "
            pdb=" OG1 THR A 166 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   SER A 278 "
            pdb=" OG1 THR A 281 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   VAL A 151 "
            pdb=" OG1 THR A 154 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   LEU A 228 "
            pdb=" OG1 THR A 232 "
     model   vdw
     2.383 3.040
  nonbonded pdb=" O   VAL A 412 "
            pdb=" OG1 THR A 415 "
     model   vdw
     2.387 3.040
  ... (remaining 24004 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.050
  Process input model:                     12.450
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
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      :  0.007   0.057   3136  Z= 0.471
  Angle     :  0.769   5.594   4269  Z= 0.463
  Chirality :  0.048   0.266    538
  Planarity :  0.005   0.029    524
  Dihedral  : 11.978  79.581   1116
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  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: -2.28 (0.34), residues: 412
  helix: -1.19 (0.24), residues: 321
  sheet:  None (None), residues: 0
  loop : -2.03 (0.57), residues: 91

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 114 
 PHE   0.015   0.002   PHE A 261 
 TYR   0.043   0.003   TYR A 299 
 ARG   0.008   0.001   ARG A 397 

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7880 (mmmt)
REVERT: A  105 ARG cc_start: 0.7068 (mpt-90) cc_final: 0.6704 (ttt-90)
REVERT: A  108 ASN cc_start: 0.6656 (m110) cc_final: 0.5520 (t0)
REVERT: A  126 GLN cc_start: 0.7441 (tp40) cc_final: 0.6918 (mm110)
REVERT: A  273 PHE cc_start: 0.5679 (t80) cc_final: 0.5403 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1545
  time to fit residues: 21.2479
Evaluate side-chains
  82 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0000
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.5584

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

Flipped N/Q/H residues before XYZ refinement:
A  32 HIS
A 108 ASN
A 318 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.167605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.138120 restraints weight = 5501.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.141167 restraints weight = 3396.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.143279 restraints weight = 2436.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3136  Z= 0.224
  Angle     :  0.665   5.908   4269  Z= 0.339
  Chirality :  0.043   0.157    538
  Planarity :  0.004   0.026    524
  Dihedral  :  5.427  26.228    441
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 13.80 %
    Favored  : 84.36 %
  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:  0.72 (0.39), residues: 412
  helix:  1.09 (0.27), residues: 328
  sheet:  None (None), residues: 0
  loop : -1.83 (0.57), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS A 114 
 PHE   0.015   0.002   PHE A 210 
 TYR   0.034   0.002   TYR A 299 
 ARG   0.003   0.000   ARG A 397 

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.6770 (m-40) cc_final: 0.5610 (t0)
REVERT: A  126 GLN cc_start: 0.7489 (tp40) cc_final: 0.6753 (mm110)
  outliers start: 6
  outliers final: 4
  residues processed: 88
  average time/residue: 0.1163
  time to fit residues: 13.1268
Evaluate side-chains
  81 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  400 VAL
Chi-restraints excluded: chain A residue  407 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0980
   chunk 28 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4031 r_free = 0.4031 target = 0.171700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.142964 restraints weight = 5420.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.145746 restraints weight = 3427.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.147838 restraints weight = 2515.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.3141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3136  Z= 0.221
  Angle     :  0.651   8.132   4269  Z= 0.326
  Chirality :  0.043   0.149    538
  Planarity :  0.003   0.022    524
  Dihedral  :  5.224  25.735    441
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.56 %
    Favored  : 80.98 %
  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:  1.38 (0.40), residues: 412
  helix:  1.56 (0.28), residues: 330
  sheet:  None (None), residues: 0
  loop : -1.72 (0.58), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS A 114 
 PHE   0.015   0.001   PHE A 210 
 TYR   0.031   0.002   TYR A 299 
 ARG   0.003   0.000   ARG A 397 

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  108 ASN cc_start: 0.6810 (m-40) cc_final: 0.5552 (t0)
REVERT: A  114 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.8077 (p-80)
REVERT: A  126 GLN cc_start: 0.7549 (tp40) cc_final: 0.6815 (mm110)
REVERT: A  202 MET cc_start: 0.8606 (mmm) cc_final: 0.8128 (tpp)
REVERT: A  273 PHE cc_start: 0.6103 (t80) cc_final: 0.5492 (t80)
REVERT: A  351 CYS cc_start: 0.7647 (p) cc_final: 0.6756 (p)
  outliers start: 8
  outliers final: 5
  residues processed: 89
  average time/residue: 0.1167
  time to fit residues: 13.1209
Evaluate side-chains
  82 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  114 HIS
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  400 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 1 optimal weight:    0.4980
   chunk 17 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 318 GLN
** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.168134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.138302 restraints weight = 5531.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.140988 restraints weight = 3634.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.142757 restraints weight = 2721.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.3666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3136  Z= 0.228
  Angle     :  0.661  10.004   4269  Z= 0.326
  Chirality :  0.043   0.158    538
  Planarity :  0.003   0.023    524
  Dihedral  :  5.171  28.558    441
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 17.18 %
    Favored  : 79.14 %
  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:  1.59 (0.41), residues: 412
  helix:  1.66 (0.28), residues: 334
  sheet:  None (None), residues: 0
  loop : -1.61 (0.62), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  32 
 PHE   0.015   0.002   PHE A 210 
 TYR   0.027   0.002   TYR A 299 
 ARG   0.004   0.001   ARG A 397 

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A   21 ILE cc_start: 0.8948 (pt) cc_final: 0.8719 (pt)
REVERT: A  105 ARG cc_start: 0.6311 (ttt90) cc_final: 0.6042 (ttt-90)
REVERT: A  126 GLN cc_start: 0.7688 (tp40) cc_final: 0.6949 (mm110)
REVERT: A  202 MET cc_start: 0.8542 (mmm) cc_final: 0.8224 (tpp)
REVERT: A  210 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7647 (t80)
REVERT: A  219 GLU cc_start: 0.7790 (tp30) cc_final: 0.7494 (mm-30)
  outliers start: 12
  outliers final: 5
  residues processed: 90
  average time/residue: 0.1259
  time to fit residues: 14.0829
Evaluate side-chains
  88 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  210 PHE
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  400 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 28 optimal weight:    0.3980
   chunk 12 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0970
   chunk 8 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 318 GLN
** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.164784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.135373 restraints weight = 5559.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.137647 restraints weight = 3764.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.139391 restraints weight = 2921.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.4067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3136  Z= 0.212
  Angle     :  0.645   9.535   4269  Z= 0.321
  Chirality :  0.043   0.153    538
  Planarity :  0.004   0.039    524
  Dihedral  :  5.166  28.282    441
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 18.40 %
    Favored  : 77.30 %
  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:  1.75 (0.41), residues: 412
  helix:  1.78 (0.28), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.49 (0.63), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  32 
 PHE   0.015   0.001   PHE A 210 
 TYR   0.026   0.002   TYR A 299 
 ARG   0.002   0.000   ARG A 397 

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A   21 ILE cc_start: 0.8995 (pt) cc_final: 0.8722 (pt)
REVERT: A  103 MET cc_start: 0.8246 (ttm) cc_final: 0.7960 (ttm)
REVERT: A  105 ARG cc_start: 0.6537 (ttt90) cc_final: 0.6190 (ttt-90)
REVERT: A  126 GLN cc_start: 0.7633 (tp40) cc_final: 0.6907 (mm110)
REVERT: A  202 MET cc_start: 0.8544 (mmm) cc_final: 0.8330 (tpp)
REVERT: A  210 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7651 (t80)
REVERT: A  362 MET cc_start: 0.7800 (mtm) cc_final: 0.7529 (mtp)
  outliers start: 14
  outliers final: 10
  residues processed: 87
  average time/residue: 0.1185
  time to fit residues: 12.9483
Evaluate side-chains
  93 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  210 PHE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  400 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 27 optimal weight:    0.4980
   chunk 2 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 13 optimal weight:    0.2980
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 318 GLN
** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.164246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.134546 restraints weight = 5674.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.136890 restraints weight = 3886.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.138527 restraints weight = 3014.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.4265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3136  Z= 0.217
  Angle     :  0.653  11.798   4269  Z= 0.320
  Chirality :  0.043   0.150    538
  Planarity :  0.003   0.023    524
  Dihedral  :  5.082  28.163    441
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.86 %
    Favored  : 75.15 %
  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:  1.82 (0.42), residues: 412
  helix:  1.82 (0.28), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.45 (0.66), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  32 
 PHE   0.015   0.001   PHE A 210 
 TYR   0.025   0.002   TYR A 299 
 ARG   0.002   0.000   ARG A 397 

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A   21 ILE cc_start: 0.9037 (pt) cc_final: 0.8790 (pt)
REVERT: A  103 MET cc_start: 0.8185 (ttm) cc_final: 0.7897 (ttm)
REVERT: A  105 ARG cc_start: 0.6510 (ttt90) cc_final: 0.6124 (ttt-90)
REVERT: A  126 GLN cc_start: 0.7634 (tp40) cc_final: 0.6930 (mm110)
REVERT: A  210 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7651 (t80)
REVERT: A  219 GLU cc_start: 0.7737 (tp30) cc_final: 0.7272 (mm-30)
  outliers start: 13
  outliers final: 8
  residues processed: 89
  average time/residue: 0.1218
  time to fit residues: 13.6247
Evaluate side-chains
  92 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  210 PHE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  400 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 35 optimal weight:    0.4980
   chunk 30 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   chunk 1 optimal weight:    0.4980
   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 318 GLN
** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.164930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.135556 restraints weight = 5563.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.138001 restraints weight = 3730.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.139640 restraints weight = 2884.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.4460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3136  Z= 0.203
  Angle     :  0.677  12.871   4269  Z= 0.329
  Chirality :  0.043   0.215    538
  Planarity :  0.004   0.048    524
  Dihedral  :  5.104  27.770    441
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 22.39 %
    Favored  : 74.23 %
  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:  1.86 (0.41), residues: 412
  helix:  1.83 (0.28), residues: 333
  sheet:  None (None), residues: 0
  loop : -1.39 (0.66), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  32 
 PHE   0.014   0.001   PHE A 210 
 TYR   0.025   0.002   TYR A 299 
 ARG   0.002   0.000   ARG A 397 

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A   21 ILE cc_start: 0.9026 (pt) cc_final: 0.8761 (pt)
REVERT: A   52 ARG cc_start: 0.8474 (tpp80) cc_final: 0.6380 (ttp-170)
REVERT: A  105 ARG cc_start: 0.6509 (ttt90) cc_final: 0.6271 (ttt-90)
REVERT: A  126 GLN cc_start: 0.7661 (tp40) cc_final: 0.6983 (mm110)
REVERT: A  210 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7593 (t80)
  outliers start: 11
  outliers final: 10
  residues processed: 91
  average time/residue: 0.1193
  time to fit residues: 13.6115
Evaluate side-chains
  92 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  210 PHE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  399 MET
Chi-restraints excluded: chain A residue  400 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0040
   chunk 18 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 35 optimal weight:    0.2980
   chunk 11 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.4592

-------------------------------------------------------------------------------
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 = 0.3972 r_free = 0.3972 target = 0.166249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.137204 restraints weight = 5593.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.139704 restraints weight = 3756.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.141366 restraints weight = 2855.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.4668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3136  Z= 0.193
  Angle     :  0.691  12.716   4269  Z= 0.332
  Chirality :  0.043   0.220    538
  Planarity :  0.003   0.024    524
  Dihedral  :  5.016  27.647    441
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 23.62 %
    Favored  : 73.01 %
  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:  1.81 (0.41), residues: 412
  helix:  1.82 (0.28), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.42 (0.65), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  32 
 PHE   0.014   0.001   PHE A 210 
 TYR   0.025   0.002   TYR A 317 
 ARG   0.001   0.000   ARG A 105 

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A   21 ILE cc_start: 0.9013 (pt) cc_final: 0.8775 (pt)
REVERT: A   52 ARG cc_start: 0.8449 (tpp80) cc_final: 0.6387 (ttp-170)
REVERT: A  103 MET cc_start: 0.8043 (ttm) cc_final: 0.7800 (ttm)
REVERT: A  114 HIS cc_start: 0.8162 (p90) cc_final: 0.7751 (p90)
REVERT: A  126 GLN cc_start: 0.7680 (tp40) cc_final: 0.7023 (mm110)
REVERT: A  269 MET cc_start: 0.8179 (tpp) cc_final: 0.7906 (tpp)
REVERT: A  276 ARG cc_start: 0.6707 (mtp85) cc_final: 0.6339 (ttp-170)
  outliers start: 11
  outliers final: 9
  residues processed: 91
  average time/residue: 0.1291
  time to fit residues: 14.6469
Evaluate side-chains
  90 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  399 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 40 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0270
   chunk 37 optimal weight:    0.3980
   chunk 22 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
A 318 GLN
** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.165374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.136394 restraints weight = 5533.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.138805 restraints weight = 3735.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.140425 restraints weight = 2868.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.4781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3136  Z= 0.203
  Angle     :  0.713  13.128   4269  Z= 0.342
  Chirality :  0.043   0.218    538
  Planarity :  0.004   0.050    524
  Dihedral  :  5.069  27.134    441
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 24.54 %
    Favored  : 71.78 %
  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:  1.99 (0.42), residues: 412
  helix:  1.94 (0.29), residues: 326
  sheet:  None (None), residues: 0
  loop : -1.11 (0.68), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  32 
 PHE   0.014   0.001   PHE A 210 
 TYR   0.045   0.002   TYR A 317 
 ARG   0.001   0.000   ARG A 276 

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A   21 ILE cc_start: 0.8905 (pt) cc_final: 0.8628 (pt)
REVERT: A   52 ARG cc_start: 0.8460 (tpp80) cc_final: 0.6397 (ttp-170)
REVERT: A  103 MET cc_start: 0.8026 (ttm) cc_final: 0.7729 (ttm)
REVERT: A  114 HIS cc_start: 0.8124 (p90) cc_final: 0.7732 (p90)
REVERT: A  126 GLN cc_start: 0.7672 (tp40) cc_final: 0.7045 (mm110)
REVERT: A  276 ARG cc_start: 0.6730 (mtp85) cc_final: 0.6303 (ttp-170)
REVERT: A  309 ILE cc_start: 0.8605 (mm) cc_final: 0.8395 (tp)
  outliers start: 12
  outliers final: 11
  residues processed: 92
  average time/residue: 0.1598
  time to fit residues: 17.8923
Evaluate side-chains
  95 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  399 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0970
   chunk 20 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0470
   chunk 31 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0030
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.3086

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

Flipped N/Q/H residues before XYZ refinement:
** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.167442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.138414 restraints weight = 5455.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.141066 restraints weight = 3629.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.142841 restraints weight = 2735.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.5047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3136  Z= 0.190
  Angle     :  0.728  13.711   4269  Z= 0.345
  Chirality :  0.045   0.223    538
  Planarity :  0.003   0.026    524
  Dihedral  :  5.080  29.196    441
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 24.54 %
    Favored  : 71.78 %
  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:  2.06 (0.43), residues: 412
  helix:  2.00 (0.29), residues: 327
  sheet:  None (None), residues: 0
  loop : -1.17 (0.68), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A 332 
 PHE   0.011   0.001   PHE A 210 
 TYR   0.047   0.002   TYR A 317 
 ARG   0.006   0.000   ARG A 397 

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 ILE cc_start: 0.8945 (pt) cc_final: 0.8669 (pt)
REVERT: A   52 ARG cc_start: 0.8373 (tpp80) cc_final: 0.6282 (ttp-170)
REVERT: A  103 MET cc_start: 0.8026 (ttm) cc_final: 0.7766 (ttm)
REVERT: A  114 HIS cc_start: 0.8046 (p90) cc_final: 0.7722 (p90)
REVERT: A  126 GLN cc_start: 0.7691 (tp40) cc_final: 0.7073 (mm110)
REVERT: A  155 ILE cc_start: 0.8285 (mt) cc_final: 0.8075 (mt)
REVERT: A  276 ARG cc_start: 0.6750 (mtp85) cc_final: 0.6315 (ttp-170)
  outliers start: 12
  outliers final: 9
  residues processed: 94
  average time/residue: 0.1400
  time to fit residues: 16.0306
Evaluate side-chains
  96 residues out of total 326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  372 LEU
Chi-restraints excluded: chain A residue  386 ILE
Chi-restraints excluded: chain A residue  399 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0980
   chunk 40 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 37 optimal weight:    0.1980
   chunk 28 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.166555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.137776 restraints weight = 5588.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.140240 restraints weight = 3709.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.142173 restraints weight = 2821.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.5288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3136  Z= 0.221
  Angle     :  0.767  13.366   4269  Z= 0.365
  Chirality :  0.048   0.307    538
  Planarity :  0.004   0.044    524
  Dihedral  :  5.241  27.505    441
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 25.15 %
    Favored  : 71.47 %
  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:  1.97 (0.43), residues: 412
  helix:  1.96 (0.29), residues: 326
  sheet:  None (None), residues: 0
  loop : -1.29 (0.67), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  32 
 PHE   0.014   0.001   PHE A 210 
 TYR   0.031   0.002   TYR A 317 
 ARG   0.006   0.000   ARG A 397 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1349.58 seconds
wall clock time: 24 minutes 6.85 seconds (1446.85 seconds total)