Starting phenix.real_space_refine
on Sat Apr 26 22:23:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kh5_62332/04_2025/9kh5_62332_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kh5_62332/04_2025/9kh5_62332.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kh5_62332/04_2025/9kh5_62332.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kh5_62332/04_2025/9kh5_62332.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kh5_62332/04_2025/9kh5_62332_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kh5_62332/04_2025/9kh5_62332_neut.cif"
  }
  resolution = 3.74
  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=   0.032
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      19      5.16       5
     C    2353      2.51       5
     N     549      2.21       5
     O     605      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3526
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3526
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 455, 3526
          Classifications: {'peptide': 455}
          Link IDs: {'PTRANS': 20, 'TRANS': 434}
  Time building chain proxies: 3.18, per 1000 atoms: 0.90
  Number of scatterers: 3526
  At special positions: 0
  Unit cell: (71.82, 87.21, 71.82, 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      19     16.00
     O     605      8.00
     N     549      7.00
     C    2353      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: 0.93
  Conformation dependent library (CDL) restraints added in 418.5 milliseconds
  

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  846

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 1 sheets defined
      78.2% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 48
      removed outlier: 4.855A  pdb=" N   CYS A  44 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   LEU A  45 " --> pdb=" O   ASN A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 56
    Processing helix  chain 'A' and resid 57 through 67
      removed outlier: 3.790A  pdb=" N   GLY A  61 " --> pdb=" O   VAL A  57 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   VAL A  62 " --> pdb=" O   SER A  58 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   LEU A  63 " --> pdb=" O   PRO A  59 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ILE A  64 " --> pdb=" O   LYS A  60 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   TYR A  65 " --> pdb=" O   GLY A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 97
      removed outlier: 3.554A  pdb=" N   THR A  95 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 113 through 126
      removed outlier: 3.982A  pdb=" N   PHE A 117 " --> pdb=" O   GLY A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 145
    Processing helix  chain 'A' and resid 154 through 174
      removed outlier: 3.535A  pdb=" N   SER A 158 " --> pdb=" O   PRO A 154 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   PHE A 171 " --> pdb=" O   CYS A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 209
      removed outlier: 3.788A  pdb=" N   TYR A 189 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   LEU A 206 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   GLY A 209 " --> pdb=" O   ARG A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 240
      removed outlier: 3.850A  pdb=" N   LEU A 230 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   SER A 238 " --> pdb=" O   SER A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 285
      removed outlier: 3.948A  pdb=" N   LEU A 261 " --> pdb=" O   ARG A 257 " (cutoff:3.500A)
      Proline residue:  A 268  - end of helix
    Processing helix  chain 'A' and resid 286 through 293
    Processing helix  chain 'A' and resid 295 through 305
      removed outlier: 3.530A  pdb=" N   THR A 299 " --> pdb=" O   ALA A 295 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ILE A 304 " --> pdb=" O   PHE A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 340
      removed outlier: 3.946A  pdb=" N   VAL A 329 " --> pdb=" O   ASN A 325 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ALA A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   ALA A 331 " --> pdb=" O   SER A 327 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   SER A 332 " --> pdb=" O   ILE A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 374
      removed outlier: 3.721A  pdb=" N   TYR A 372 " --> pdb=" O   MET A 368 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   CYS A 374 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 406
      removed outlier: 3.591A  pdb=" N   LEU A 381 " --> pdb=" O   ASP A 377 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER A 388 " --> pdb=" O   TYR A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 434
    Processing helix  chain 'A' and resid 439 through 461
      removed outlier: 3.980A  pdb=" N   SER A 443 " --> pdb=" O   ASP A 439 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LEU A 454 " --> pdb=" O   ALA A 450 " (cutoff:3.500A)
      Proline residue:  A 455  - end of helix
    Processing helix  chain 'A' and resid 466 through 488
    Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 352

    248 hydrogen bonds defined for protein.
    738 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: 1.23

  Time building geometry restraints manager: 1.11 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: 1049
        1.34 -     1.46: 805
        1.46 -     1.57: 1740
        1.57 -     1.69: 0
        1.69 -     1.81: 26
  Bond restraints: 3620
  Sorted by residual:
  bond pdb=" C   TYR A  65 "
       pdb=" N   SER A  66 "
    ideal  model  delta    sigma   weight residual
    1.331  1.299  0.032 1.40e-02 5.10e+03 5.35e+00
  bond pdb=" C   PHE A 148 "
       pdb=" N   PRO A 149 "
    ideal  model  delta    sigma   weight residual
    1.334  1.313  0.021 1.11e-02 8.12e+03 3.55e+00
  bond pdb=" C   ARG A 468 "
       pdb=" O   ARG A 468 "
    ideal  model  delta    sigma   weight residual
    1.244  1.228  0.016 9.80e-03 1.04e+04 2.53e+00
  bond pdb=" C   ALA A 110 "
       pdb=" N   PHE A 111 "
    ideal  model  delta    sigma   weight residual
    1.332  1.311  0.021 1.40e-02 5.10e+03 2.31e+00
  bond pdb=" CA  GLN A 380 "
       pdb=" C   GLN A 380 "
    ideal  model  delta    sigma   weight residual
    1.524  1.506  0.019 1.28e-02 6.10e+03 2.15e+00
  ... (remaining 3615 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 4614
        1.74 -     3.49: 262
        3.49 -     5.23: 50
        5.23 -     6.98: 12
        6.98 -     8.72: 3
  Bond angle restraints: 4941
  Sorted by residual:
  angle pdb=" CA  SER A 217 "
        pdb=" C   SER A 217 "
        pdb=" N   PHE A 218 "
      ideal   model   delta    sigma   weight residual
     119.46  115.85    3.61 6.10e-01 2.69e+00 3.51e+01
  angle pdb=" C   GLU A 256 "
        pdb=" CA  GLU A 256 "
        pdb=" CB  GLU A 256 "
      ideal   model   delta    sigma   weight residual
     116.54  110.18    6.36 1.15e+00 7.56e-01 3.06e+01
  angle pdb=" C   LYS A 467 "
        pdb=" CA  LYS A 467 "
        pdb=" CB  LYS A 467 "
      ideal   model   delta    sigma   weight residual
     115.89  109.49    6.40 1.32e+00 5.74e-01 2.35e+01
  angle pdb=" N   CYS A 174 "
        pdb=" CA  CYS A 174 "
        pdb=" C   CYS A 174 "
      ideal   model   delta    sigma   weight residual
     112.54  106.99    5.55 1.22e+00 6.72e-01 2.07e+01
  angle pdb=" N   PHE A 356 "
        pdb=" CA  PHE A 356 "
        pdb=" C   PHE A 356 "
      ideal   model   delta    sigma   weight residual
     111.90  106.93    4.97 1.32e+00 5.74e-01 1.42e+01
  ... (remaining 4936 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.85: 1784
       16.85 -    33.70: 215
       33.70 -    50.55: 65
       50.55 -    67.40: 22
       67.40 -    84.25: 3
  Dihedral angle restraints: 2089
    sinusoidal: 766
      harmonic: 1323
  Sorted by residual:
  dihedral pdb=" CA  GLN A 303 "
           pdb=" C   GLN A 303 "
           pdb=" N   ILE A 304 "
           pdb=" CA  ILE A 304 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.15  -26.85     0      5.00e+00 4.00e-02 2.88e+01
  dihedral pdb=" CA  ILE A 126 "
           pdb=" C   ILE A 126 "
           pdb=" N   ILE A 127 "
           pdb=" CA  ILE A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.52  -23.48     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  LYS A 406 "
           pdb=" C   LYS A 406 "
           pdb=" N   GLU A 407 "
           pdb=" CA  GLU A 407 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.77  -20.23     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 2086 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 351
       0.034 -    0.069: 168
       0.069 -    0.103: 46
       0.103 -    0.137: 17
       0.137 -    0.172: 4
  Chirality restraints: 586
  Sorted by residual:
  chirality pdb=" CB  ILE A 228 "
            pdb=" CA  ILE A 228 "
            pdb=" CG1 ILE A 228 "
            pdb=" CG2 ILE A 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.37e-01
  chirality pdb=" CA  PHE A 218 "
            pdb=" N   PHE A 218 "
            pdb=" C   PHE A 218 "
            pdb=" CB  PHE A 218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.05e-01
  chirality pdb=" CA  GLU A 128 "
            pdb=" N   GLU A 128 "
            pdb=" C   GLU A 128 "
            pdb=" CB  GLU A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.43e-01
  ... (remaining 583 not shown)

  Planarity restraints: 604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 482 "    0.009 2.00e-02 2.50e+03   1.87e-02 3.50e+00
        pdb=" C   TYR A 482 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   TYR A 482 "    0.012 2.00e-02 2.50e+03
        pdb=" N   LEU A 483 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  58 "   -0.029 5.00e-02 4.00e+02   4.42e-02 3.12e+00
        pdb=" N   PRO A  59 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A  59 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A  59 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 384 "   -0.013 2.00e-02 2.50e+03   1.22e-02 2.97e+00
        pdb=" CG  TYR A 384 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 384 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 384 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 384 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 384 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 384 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR A 384 "    0.003 2.00e-02 2.50e+03
  ... (remaining 601 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 979
        2.77 -     3.30: 4288
        3.30 -     3.83: 6402
        3.83 -     4.37: 7474
        4.37 -     4.90: 10943
  Nonbonded interactions: 30086
  Sorted by model distance:
  nonbonded pdb=" O   GLY A  54 "
            pdb=" OG  SER A  58 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   PRO A 358 "
            pdb=" OG  SER A 361 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   ILE A 449 "
            pdb=" OG  SER A 452 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   VAL A 329 "
            pdb=" OG  SER A 332 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   PHE A  69 "
            pdb=" OG  SER A  72 "
     model   vdw
     2.268 3.040
  ... (remaining 30081 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:             1.420
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     14.540
  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:3.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.061   3620  Z= 0.390
  Angle     :  0.983   8.722   4941  Z= 0.600
  Chirality :  0.045   0.172    586
  Planarity :  0.005   0.044    604
  Dihedral  : 17.148  84.248   1243
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 28.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.02 %
    Favored  : 86.98 %
  Rotamer:
    Outliers :  8.97 %
    Allowed  : 14.51 %
    Favored  : 76.52 %
  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: -4.34 (0.32), residues: 453
  helix: -2.10 (0.24), residues: 321
  sheet:  None (None), residues: 0
  loop : -4.60 (0.38), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 390 
 HIS   0.003   0.001   HIS A 352 
 PHE   0.015   0.002   PHE A 430 
 TYR   0.030   0.002   TYR A 384 
 ARG   0.004   0.000   ARG A 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17153 (  248)
  hydrogen bonds       : angle       7.22394 (  738)
  covalent geometry    : bond        0.00754 ( 3620)
  covalent geometry    : angle       0.98253 ( 4941)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 77
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ARG cc_start: 0.9520 (mmp-170) cc_final: 0.9281 (mmm160)
REVERT: A  167 CYS cc_start: 0.9468 (t) cc_final: 0.8936 (p)
REVERT: A  168 LEU cc_start: 0.9759 (tt) cc_final: 0.9170 (mp)
REVERT: A  223 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.6790 (t80)
REVERT: A  240 SER cc_start: 0.7013 (p) cc_final: 0.6765 (m)
REVERT: A  247 TYR cc_start: 0.7867 (t80) cc_final: 0.7469 (t80)
  outliers start: 34
  outliers final: 12
  residues processed: 105
  average time/residue: 0.1767
  time to fit residues: 22.3026
Evaluate side-chains
  77 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  289 ASP
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  465 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:   20.0000
   chunk 34 optimal weight:    0.8980
   chunk 18 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0370
   chunk 26 optimal weight:    2.9990
   chunk 40 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   overall best weight:    1.3862

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

Flipped N/Q/H residues before XYZ refinement:
A 246 ASN
** A 484 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 = 0.3531 r_free = 0.3531 target = 0.075386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.061253 restraints weight = 17584.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.063037 restraints weight = 10577.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.064291 restraints weight = 7458.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.2797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3620  Z= 0.194
  Angle     :  0.821   7.150   4941  Z= 0.421
  Chirality :  0.046   0.180    586
  Planarity :  0.006   0.056    604
  Dihedral  :  9.604  57.450    523
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 17.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.39 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 19.53 %
    Favored  : 74.93 %
  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: -2.37 (0.34), residues: 453
  helix: -0.50 (0.26), residues: 325
  sheet:  None (None), residues: 0
  loop : -4.35 (0.35), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 179 
 HIS   0.005   0.002   HIS A 466 
 PHE   0.026   0.002   PHE A 392 
 TYR   0.029   0.003   TYR A 239 
 ARG   0.005   0.001   ARG A 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06456 (  248)
  hydrogen bonds       : angle       5.39048 (  738)
  covalent geometry    : bond        0.00406 ( 3620)
  covalent geometry    : angle       0.82144 ( 4941)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.8532 (tpt) cc_final: 0.8295 (tpp)
REVERT: A  121 TRP cc_start: 0.9427 (t-100) cc_final: 0.9149 (t-100)
REVERT: A  167 CYS cc_start: 0.9253 (t) cc_final: 0.8872 (p)
REVERT: A  168 LEU cc_start: 0.9721 (tt) cc_final: 0.9218 (mp)
REVERT: A  178 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8084 (pttt)
REVERT: A  184 GLN cc_start: 0.9319 (pt0) cc_final: 0.9103 (pp30)
REVERT: A  223 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.6685 (t80)
REVERT: A  240 SER cc_start: 0.6795 (p) cc_final: 0.6435 (m)
REVERT: A  247 TYR cc_start: 0.7980 (t80) cc_final: 0.7513 (t80)
REVERT: A  252 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7595 (tp)
REVERT: A  303 GLN cc_start: 0.9369 (tp40) cc_final: 0.8928 (tt0)
REVERT: A  472 LEU cc_start: 0.9344 (mt) cc_final: 0.9109 (pp)
  outliers start: 21
  outliers final: 11
  residues processed: 97
  average time/residue: 0.1433
  time to fit residues: 17.1815
Evaluate side-chains
  79 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  465 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 38 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 26 optimal weight:    9.9990
   chunk 8 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 484 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 = 0.3523 r_free = 0.3523 target = 0.075102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.061173 restraints weight = 17069.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.062944 restraints weight = 10589.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.064138 restraints weight = 7504.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3620  Z= 0.171
  Angle     :  0.759   7.752   4941  Z= 0.386
  Chirality :  0.044   0.182    586
  Planarity :  0.005   0.056    604
  Dihedral  :  8.642  57.246    513
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 16.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 22.69 %
    Favored  : 72.30 %
  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: -1.28 (0.38), residues: 453
  helix:  0.34 (0.28), residues: 330
  sheet:  None (None), residues: 0
  loop : -4.22 (0.39), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 179 
 HIS   0.002   0.001   HIS A 343 
 PHE   0.021   0.002   PHE A 392 
 TYR   0.021   0.002   TYR A 176 
 ARG   0.004   0.001   ARG A 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05429 (  248)
  hydrogen bonds       : angle       5.17089 (  738)
  covalent geometry    : bond        0.00362 ( 3620)
  covalent geometry    : angle       0.75873 ( 4941)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ARG cc_start: 0.9432 (mmp-170) cc_final: 0.9063 (mmp-170)
REVERT: A  121 TRP cc_start: 0.9406 (t-100) cc_final: 0.9186 (t-100)
REVERT: A  167 CYS cc_start: 0.9222 (t) cc_final: 0.8832 (p)
REVERT: A  168 LEU cc_start: 0.9724 (tt) cc_final: 0.9116 (mp)
REVERT: A  223 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6407 (t80)
REVERT: A  247 TYR cc_start: 0.8017 (t80) cc_final: 0.7669 (t80)
REVERT: A  303 GLN cc_start: 0.9386 (tp40) cc_final: 0.8929 (tt0)
REVERT: A  305 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.8028 (m-10)
REVERT: A  378 ILE cc_start: 0.9364 (mp) cc_final: 0.9021 (tp)
REVERT: A  392 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.6996 (m-80)
REVERT: A  403 LEU cc_start: 0.9664 (tp) cc_final: 0.9450 (pp)
  outliers start: 19
  outliers final: 10
  residues processed: 85
  average time/residue: 0.1554
  time to fit residues: 16.2639
Evaluate side-chains
  73 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 TRP
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  305 PHE
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  462 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 37 optimal weight:    9.9990
   chunk 28 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 11 optimal weight:    0.0570
   chunk 24 optimal weight:   10.0000
   overall best weight:    0.9302

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

Flipped N/Q/H residues before XYZ refinement:
** A 484 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 = 0.3545 r_free = 0.3545 target = 0.076574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.062192 restraints weight = 17405.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.063958 restraints weight = 10701.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.065225 restraints weight = 7608.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.4245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3620  Z= 0.154
  Angle     :  0.740   6.887   4941  Z= 0.372
  Chirality :  0.044   0.174    586
  Planarity :  0.005   0.046    604
  Dihedral  :  7.939  56.234    509
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 25.07 %
    Favored  : 70.18 %
  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: -0.87 (0.38), residues: 453
  helix:  0.59 (0.28), residues: 331
  sheet:  None (None), residues: 0
  loop : -3.93 (0.40), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 179 
 HIS   0.001   0.000   HIS A 343 
 PHE   0.018   0.001   PHE A 392 
 TYR   0.025   0.002   TYR A  65 
 ARG   0.007   0.001   ARG A 410 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04881 (  248)
  hydrogen bonds       : angle       4.96479 (  738)
  covalent geometry    : bond        0.00335 ( 3620)
  covalent geometry    : angle       0.73968 ( 4941)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ARG cc_start: 0.9390 (mmp-170) cc_final: 0.8974 (mmp-170)
REVERT: A  121 TRP cc_start: 0.9411 (t-100) cc_final: 0.9180 (t-100)
REVERT: A  167 CYS cc_start: 0.9203 (t) cc_final: 0.8841 (p)
REVERT: A  168 LEU cc_start: 0.9687 (tt) cc_final: 0.9172 (mp)
REVERT: A  223 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.6302 (t80)
REVERT: A  227 ASP cc_start: 0.7351 (p0) cc_final: 0.6777 (p0)
REVERT: A  247 TYR cc_start: 0.8015 (t80) cc_final: 0.7693 (t80)
REVERT: A  378 ILE cc_start: 0.9446 (mp) cc_final: 0.9108 (tp)
REVERT: A  392 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.6864 (m-80)
  outliers start: 18
  outliers final: 11
  residues processed: 78
  average time/residue: 0.1297
  time to fit residues: 12.9424
Evaluate side-chains
  78 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  179 TRP
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain A residue  463 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 41 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 484 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 = 0.3529 r_free = 0.3529 target = 0.075317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.061026 restraints weight = 17800.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 16)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.062774 restraints weight = 10891.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.064014 restraints weight = 7771.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.4506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3620  Z= 0.160
  Angle     :  0.722   8.883   4941  Z= 0.364
  Chirality :  0.043   0.180    586
  Planarity :  0.005   0.045    604
  Dihedral  :  7.753  55.773    507
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 25.33 %
    Favored  : 69.92 %
  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: -0.47 (0.40), residues: 453
  helix:  0.85 (0.29), residues: 327
  sheet:  None (None), residues: 0
  loop : -3.55 (0.46), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 179 
 HIS   0.001   0.001   HIS A 352 
 PHE   0.018   0.001   PHE A 392 
 TYR   0.016   0.002   TYR A  65 
 ARG   0.002   0.000   ARG A 462 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04768 (  248)
  hydrogen bonds       : angle       4.89879 (  738)
  covalent geometry    : bond        0.00352 ( 3620)
  covalent geometry    : angle       0.72208 ( 4941)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 67
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ARG cc_start: 0.9381 (mmp-170) cc_final: 0.8949 (mmp-170)
REVERT: A  167 CYS cc_start: 0.9203 (t) cc_final: 0.8771 (p)
REVERT: A  168 LEU cc_start: 0.9702 (tt) cc_final: 0.9204 (mp)
REVERT: A  223 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6136 (t80)
REVERT: A  227 ASP cc_start: 0.7527 (p0) cc_final: 0.6967 (p0)
REVERT: A  378 ILE cc_start: 0.9459 (mp) cc_final: 0.9122 (tp)
REVERT: A  392 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.6890 (m-80)
  outliers start: 18
  outliers final: 13
  residues processed: 79
  average time/residue: 0.1474
  time to fit residues: 14.7181
Evaluate side-chains
  77 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  179 TRP
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain A residue  463 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 44 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 25 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 484 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 = 0.3448 r_free = 0.3448 target = 0.071576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.057067 restraints weight = 18537.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.058784 restraints weight = 11271.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.059570 restraints weight = 7924.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.4626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3620  Z= 0.197
  Angle     :  0.758  11.321   4941  Z= 0.382
  Chirality :  0.043   0.174    586
  Planarity :  0.006   0.055    604
  Dihedral  :  7.836  54.826    507
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 17.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  7.65 %
    Allowed  : 25.07 %
    Favored  : 67.28 %
  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: -0.50 (0.40), residues: 453
  helix:  0.87 (0.29), residues: 326
  sheet:  None (None), residues: 0
  loop : -3.65 (0.46), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 242 
 HIS   0.002   0.001   HIS A 352 
 PHE   0.021   0.001   PHE A 392 
 TYR   0.016   0.002   TYR A 155 
 ARG   0.004   0.001   ARG A 462 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04992 (  248)
  hydrogen bonds       : angle       4.95588 (  738)
  covalent geometry    : bond        0.00448 ( 3620)
  covalent geometry    : angle       0.75755 ( 4941)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 62
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 LYS cc_start: 0.7588 (mmmt) cc_final: 0.7091 (mmtt)
REVERT: A  167 CYS cc_start: 0.9234 (t) cc_final: 0.8818 (p)
REVERT: A  168 LEU cc_start: 0.9728 (OUTLIER) cc_final: 0.9229 (mp)
REVERT: A  223 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.6016 (t80)
REVERT: A  303 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.9143 (mm-40)
REVERT: A  350 MET cc_start: 0.8946 (tpp) cc_final: 0.7895 (tpp)
REVERT: A  378 ILE cc_start: 0.9476 (mp) cc_final: 0.9160 (tp)
  outliers start: 29
  outliers final: 18
  residues processed: 83
  average time/residue: 0.1363
  time to fit residues: 14.3424
Evaluate side-chains
  84 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 63
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  179 TRP
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain A residue  463 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 24 optimal weight:    0.4980
   chunk 31 optimal weight:    8.9990
   chunk 6 optimal weight:    8.9990
   chunk 19 optimal weight:    8.9990
   chunk 16 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   overall best weight:    4.4988

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

Flipped N/Q/H residues before XYZ refinement:
** A 484 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 = 0.3406 r_free = 0.3406 target = 0.070103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.056047 restraints weight = 18550.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.057622 restraints weight = 11109.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.058815 restraints weight = 7918.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.4838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   3620  Z= 0.220
  Angle     :  0.784   9.754   4941  Z= 0.393
  Chirality :  0.044   0.179    586
  Planarity :  0.005   0.047    604
  Dihedral  :  7.890  52.604    507
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 17.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  7.39 %
    Allowed  : 27.18 %
    Favored  : 65.44 %
  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: -0.36 (0.39), residues: 453
  helix:  1.04 (0.29), residues: 317
  sheet:  None (None), residues: 0
  loop : -3.50 (0.45), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 179 
 HIS   0.002   0.000   HIS A 343 
 PHE   0.018   0.001   PHE A 392 
 TYR   0.018   0.002   TYR A 106 
 ARG   0.004   0.001   ARG A 462 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05141 (  248)
  hydrogen bonds       : angle       5.01694 (  738)
  covalent geometry    : bond        0.00495 ( 3620)
  covalent geometry    : angle       0.78429 ( 4941)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 63
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 CYS cc_start: 0.9284 (t) cc_final: 0.8820 (p)
REVERT: A  168 LEU cc_start: 0.9746 (OUTLIER) cc_final: 0.9196 (mp)
REVERT: A  350 MET cc_start: 0.9005 (tpp) cc_final: 0.7921 (tpp)
REVERT: A  378 ILE cc_start: 0.9466 (mp) cc_final: 0.9165 (tp)
  outliers start: 28
  outliers final: 22
  residues processed: 80
  average time/residue: 0.1388
  time to fit residues: 13.9732
Evaluate side-chains
  82 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 59
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  179 TRP
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  289 ASP
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  462 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 43 optimal weight:    6.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A 484 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 = 0.3444 r_free = 0.3444 target = 0.072207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.057988 restraints weight = 18310.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.059577 restraints weight = 10885.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.060877 restraints weight = 7746.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.5142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3620  Z= 0.155
  Angle     :  0.786  11.259   4941  Z= 0.384
  Chirality :  0.044   0.183    586
  Planarity :  0.005   0.046    604
  Dihedral  :  7.700  53.518    507
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 30.08 %
    Favored  : 64.91 %
  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: -0.26 (0.40), residues: 453
  helix:  1.11 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -3.46 (0.45), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 390 
 HIS   0.001   0.000   HIS A 343 
 PHE   0.020   0.001   PHE A 392 
 TYR   0.018   0.002   TYR A 247 
 ARG   0.003   0.000   ARG A 462 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04864 (  248)
  hydrogen bonds       : angle       4.81626 (  738)
  covalent geometry    : bond        0.00341 ( 3620)
  covalent geometry    : angle       0.78587 ( 4941)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 CYS cc_start: 0.9272 (t) cc_final: 0.8814 (p)
REVERT: A  168 LEU cc_start: 0.9724 (tt) cc_final: 0.9188 (mp)
REVERT: A  227 ASP cc_start: 0.7435 (p0) cc_final: 0.6955 (p0)
REVERT: A  350 MET cc_start: 0.9037 (tpp) cc_final: 0.7906 (tpp)
REVERT: A  378 ILE cc_start: 0.9407 (mp) cc_final: 0.9117 (tt)
  outliers start: 19
  outliers final: 18
  residues processed: 76
  average time/residue: 0.1339
  time to fit residues: 12.8511
Evaluate side-chains
  78 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  179 TRP
Chi-restraints excluded: chain A residue  214 PHE
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain A residue  463 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 30 optimal weight:    0.0070
   chunk 37 optimal weight:    8.9990
   chunk 31 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 20 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    2.0006

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

Flipped N/Q/H residues before XYZ refinement:
** A 484 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 = 0.3441 r_free = 0.3441 target = 0.071903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.057991 restraints weight = 17815.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.059586 restraints weight = 10603.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.060831 restraints weight = 7553.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.5281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3620  Z= 0.154
  Angle     :  0.786  10.047   4941  Z= 0.382
  Chirality :  0.044   0.177    586
  Planarity :  0.006   0.069    604
  Dihedral  :  7.391  53.879    507
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 30.87 %
    Favored  : 64.38 %
  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: -0.10 (0.40), residues: 453
  helix:  1.24 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -3.44 (0.45), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 390 
 HIS   0.001   0.000   HIS A 343 
 PHE   0.024   0.001   PHE A 392 
 TYR   0.015   0.001   TYR A 233 
 ARG   0.003   0.000   ARG A 462 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04740 (  248)
  hydrogen bonds       : angle       4.73923 (  738)
  covalent geometry    : bond        0.00345 ( 3620)
  covalent geometry    : angle       0.78591 ( 4941)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 CYS cc_start: 0.9251 (t) cc_final: 0.8756 (p)
REVERT: A  168 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9195 (mp)
REVERT: A  227 ASP cc_start: 0.7452 (p0) cc_final: 0.6986 (p0)
REVERT: A  350 MET cc_start: 0.9066 (tpp) cc_final: 0.7947 (tpp)
REVERT: A  378 ILE cc_start: 0.9365 (mp) cc_final: 0.9067 (tt)
  outliers start: 18
  outliers final: 16
  residues processed: 76
  average time/residue: 0.1274
  time to fit residues: 12.4166
Evaluate side-chains
  75 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  179 TRP
Chi-restraints excluded: chain A residue  214 PHE
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain A residue  463 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 33 optimal weight:    8.9990
   chunk 18 optimal weight:   40.0000
   chunk 31 optimal weight:   30.0000
   chunk 10 optimal weight:    0.9990
   chunk 32 optimal weight:   20.0000
   chunk 12 optimal weight:    0.6980
   chunk 40 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 484 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 = 0.3438 r_free = 0.3438 target = 0.071393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.057736 restraints weight = 18106.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.059320 restraints weight = 10725.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.060589 restraints weight = 7634.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.5347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3620  Z= 0.164
  Angle     :  0.806  11.353   4941  Z= 0.393
  Chirality :  0.045   0.176    586
  Planarity :  0.006   0.064    604
  Dihedral  :  7.004  55.202    505
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 17.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 31.66 %
    Favored  : 63.85 %
  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: -0.08 (0.40), residues: 453
  helix:  1.27 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -3.46 (0.45), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 390 
 HIS   0.001   0.000   HIS A 343 
 PHE   0.025   0.001   PHE A 237 
 TYR   0.017   0.001   TYR A 233 
 ARG   0.003   0.000   ARG A 462 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04787 (  248)
  hydrogen bonds       : angle       4.76252 (  738)
  covalent geometry    : bond        0.00372 ( 3620)
  covalent geometry    : angle       0.80649 ( 4941)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 CYS cc_start: 0.9240 (t) cc_final: 0.8805 (p)
REVERT: A  168 LEU cc_start: 0.9725 (OUTLIER) cc_final: 0.9200 (mp)
REVERT: A  227 ASP cc_start: 0.7444 (p0) cc_final: 0.6976 (p0)
REVERT: A  350 MET cc_start: 0.9080 (tpp) cc_final: 0.8142 (tpp)
REVERT: A  378 ILE cc_start: 0.9378 (mp) cc_final: 0.9102 (tt)
  outliers start: 17
  outliers final: 16
  residues processed: 75
  average time/residue: 0.1669
  time to fit residues: 16.3079
Evaluate side-chains
  77 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  179 TRP
Chi-restraints excluded: chain A residue  214 PHE
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  462 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 8 optimal weight:    8.9990
   chunk 30 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 29 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 484 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 = 0.3456 r_free = 0.3456 target = 0.072579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.058367 restraints weight = 18120.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.060224 restraints weight = 10686.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.061424 restraints weight = 7396.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.5542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3620  Z= 0.151
  Angle     :  0.845  14.613   4941  Z= 0.401
  Chirality :  0.047   0.334    586
  Planarity :  0.006   0.062    604
  Dihedral  :  6.934  55.776    505
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 16.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 30.87 %
    Favored  : 64.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.05 (0.40), residues: 453
  helix:  1.33 (0.29), residues: 317
  sheet:  None (None), residues: 0
  loop : -3.52 (0.45), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 390 
 HIS   0.001   0.000   HIS A 343 
 PHE   0.021   0.001   PHE A 392 
 TYR   0.015   0.001   TYR A 233 
 ARG   0.003   0.000   ARG A 288 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04564 (  248)
  hydrogen bonds       : angle       4.69693 (  738)
  covalent geometry    : bond        0.00339 ( 3620)
  covalent geometry    : angle       0.84464 ( 4941)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1496.88 seconds
wall clock time: 26 minutes 46.19 seconds (1606.19 seconds total)