Starting phenix.real_space_refine
on Wed Jul  1 20:41:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vam_64901/07_2026/9vam_64901.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vam_64901/07_2026/9vam_64901.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vam_64901/07_2026/9vam_64901.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vam_64901/07_2026/9vam_64901.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vam_64901/07_2026/9vam_64901.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vam_64901/07_2026/9vam_64901.map"
  }
  resolution = 3.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.000
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       6      5.16       5
     C     537      2.51       5
     N     165      2.21       5
     O     144      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 852
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "AC"
      Number of atoms: 284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 284
          Classifications: {'peptide': 35}
          Link IDs: {'PTRANS': 1, 'TRANS': 33}
  Restraints were copied for chains:
    AA, AB
  Time building chain proxies: 0.16, per 1000 atoms: 0.19
  Number of scatterers: 852
  At special positions: 0
  Unit cell: (64.74, 48.97, 25.73, 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       6     16.00
     O     144      8.00
     N     165      7.00
     C     537      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: 0.03
  Conformation dependent library (CDL) restraints added in 18.7 milliseconds
  

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  204

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 3 sheets defined
      0.0% alpha, 28.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.02
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'AC' and resid 383 through 384
    Processing sheet with id=AA2, first strand: chain 'AC' and resid 389 through 392
    Processing sheet with id=AA3, first strand: chain 'AC' and resid 395 through 401
      removed outlier: 6.864A  pdb=" N   ARGAC 395 " --> pdb=" O   ALAAA 396 " (cutoff:3.500A)
      removed outlier: 8.152A  pdb=" N   VALAA 398 " --> pdb=" O   ARGAC 395 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ARGAC 397 " --> pdb=" O   VALAA 398 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   VALAA 400 " --> pdb=" O   ARGAC 397 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   GLNAC 399 " --> pdb=" O   VALAA 400 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ARGAA 395 " --> pdb=" O   ALAAB 396 " (cutoff:3.500A)
      removed outlier: 7.848A  pdb=" N   VALAB 398 " --> pdb=" O   ARGAA 395 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   ARGAA 397 " --> pdb=" O   VALAB 398 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   VALAB 400 " --> pdb=" O   ARGAA 397 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   GLNAA 399 " --> pdb=" O   VALAB 400 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3

    8 hydrogen bonds defined for protein.
    24 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: 0.05

  Time building geometry restraints manager: 0.05 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: 288
        1.34 -     1.45: 108
        1.45 -     1.57: 462
        1.57 -     1.69: 0
        1.69 -     1.80: 12
  Bond restraints: 870
  Sorted by residual:
  bond pdb=" CG  LEUAB 377 "
       pdb=" CD2 LEUAB 377 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.85e-01
  bond pdb=" CG  LEUAC 377 "
       pdb=" CD2 LEUAC 377 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.85e-01
  bond pdb=" CG  LEUAA 377 "
       pdb=" CD2 LEUAA 377 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.85e-01
  bond pdb=" CA  ASNAA 374 "
       pdb=" C   ASNAA 374 "
    ideal  model  delta    sigma   weight residual
    1.532  1.521  0.011 1.21e-02 6.83e+03 8.78e-01
  bond pdb=" CA  ASNAC 374 "
       pdb=" C   ASNAC 374 "
    ideal  model  delta    sigma   weight residual
    1.532  1.521  0.011 1.21e-02 6.83e+03 8.78e-01
  ... (remaining 865 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 1083
        1.61 -     3.21: 81
        3.21 -     4.82: 12
        4.82 -     6.42: 3
        6.42 -     8.02: 6
  Bond angle restraints: 1185
  Sorted by residual:
  angle pdb=" N   ALAAC 385 "
        pdb=" CA  ALAAC 385 "
        pdb=" C   ALAAC 385 "
      ideal   model   delta    sigma   weight residual
     108.38  116.40   -8.02 1.35e+00 5.49e-01 3.53e+01
  angle pdb=" N   ALAAA 385 "
        pdb=" CA  ALAAA 385 "
        pdb=" C   ALAAA 385 "
      ideal   model   delta    sigma   weight residual
     108.38  116.40   -8.02 1.35e+00 5.49e-01 3.53e+01
  angle pdb=" N   ALAAB 385 "
        pdb=" CA  ALAAB 385 "
        pdb=" C   ALAAB 385 "
      ideal   model   delta    sigma   weight residual
     108.38  116.40   -8.02 1.35e+00 5.49e-01 3.53e+01
  angle pdb=" CA  TRPAB 381 "
        pdb=" CB  TRPAB 381 "
        pdb=" CG  TRPAB 381 "
      ideal   model   delta    sigma   weight residual
     113.60  121.30   -7.70 1.90e+00 2.77e-01 1.64e+01
  angle pdb=" CA  TRPAA 381 "
        pdb=" CB  TRPAA 381 "
        pdb=" CG  TRPAA 381 "
      ideal   model   delta    sigma   weight residual
     113.60  121.30   -7.70 1.90e+00 2.77e-01 1.64e+01
  ... (remaining 1180 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     7.26: 372
        7.26 -    14.52: 78
       14.52 -    21.78: 39
       21.78 -    29.04: 15
       29.04 -    36.30: 9
  Dihedral angle restraints: 513
    sinusoidal: 201
      harmonic: 312
  Sorted by residual:
  dihedral pdb=" CA  TRPAC 381 "
           pdb=" C   TRPAC 381 "
           pdb=" N   ASNAC 382 "
           pdb=" CA  ASNAC 382 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.39   27.61     0      5.00e+00 4.00e-02 3.05e+01
  dihedral pdb=" CA  TRPAB 381 "
           pdb=" C   TRPAB 381 "
           pdb=" N   ASNAB 382 "
           pdb=" CA  ASNAB 382 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.39   27.61     0      5.00e+00 4.00e-02 3.05e+01
  dihedral pdb=" CA  TRPAA 381 "
           pdb=" C   TRPAA 381 "
           pdb=" N   ASNAA 382 "
           pdb=" CA  ASNAA 382 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.39   27.61     0      5.00e+00 4.00e-02 3.05e+01
  ... (remaining 510 not shown)

  Histogram of chiral volume deviations from ideal:
       0.003 -    0.043: 60
       0.043 -    0.083: 33
       0.083 -    0.123: 33
       0.123 -    0.164: 0
       0.164 -    0.204: 6
  Chirality restraints: 132
  Sorted by residual:
  chirality pdb=" CA  TRPAC 381 "
            pdb=" N   TRPAC 381 "
            pdb=" C   TRPAC 381 "
            pdb=" CB  TRPAC 381 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  TRPAA 381 "
            pdb=" N   TRPAA 381 "
            pdb=" C   TRPAA 381 "
            pdb=" CB  TRPAA 381 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  TRPAB 381 "
            pdb=" N   TRPAB 381 "
            pdb=" C   TRPAB 381 "
            pdb=" CB  TRPAB 381 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 129 not shown)

  Planarity restraints: 153
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRPAA 381 "   -0.038 2.00e-02 2.50e+03   3.37e-02 2.83e+01
        pdb=" CG  TRPAA 381 "    0.091 2.00e-02 2.50e+03
        pdb=" CD1 TRPAA 381 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD2 TRPAA 381 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRPAA 381 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRPAA 381 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRPAA 381 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ2 TRPAA 381 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRPAA 381 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRPAA 381 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRPAC 381 "   -0.038 2.00e-02 2.50e+03   3.37e-02 2.83e+01
        pdb=" CG  TRPAC 381 "    0.091 2.00e-02 2.50e+03
        pdb=" CD1 TRPAC 381 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD2 TRPAC 381 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRPAC 381 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRPAC 381 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRPAC 381 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ2 TRPAC 381 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRPAC 381 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRPAC 381 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRPAB 381 "   -0.038 2.00e-02 2.50e+03   3.37e-02 2.83e+01
        pdb=" CG  TRPAB 381 "    0.091 2.00e-02 2.50e+03
        pdb=" CD1 TRPAB 381 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD2 TRPAB 381 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRPAB 381 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRPAB 381 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRPAB 381 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ2 TRPAB 381 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRPAB 381 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRPAB 381 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 150 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 255
        2.84 -     3.35: 722
        3.35 -     3.87: 1330
        3.87 -     4.38: 1367
        4.38 -     4.90: 2708
  Nonbonded interactions: 6382
  Sorted by model distance:
  nonbonded pdb=" O   SERAC 378 "
            pdb=" OG  SERAC 378 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" O   SERAB 378 "
            pdb=" OG  SERAB 378 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" O   SERAA 378 "
            pdb=" OG  SERAA 378 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" O   HISAA 386 "
            pdb=" N   SERAB 387 "
     model   vdw
     2.463 3.120
  nonbonded pdb=" O   ARGAA 397 "
            pdb=" N   VALAB 398 "
     model   vdw
     2.478 3.120
  ... (remaining 6377 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'AC'
  selection = chain 'AA'
  selection = chain 'AB'
}

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:             2.630
  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:          0.010
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     1.800
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:0.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
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      :  0.005   0.031    870  Z= 0.265
  Angle     :  1.079   8.025   1185  Z= 0.676
  Chirality :  0.075   0.204    132
  Planarity :  0.010   0.057    153
  Dihedral  : 11.916  36.295    309
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.12 %
    Favored  : 87.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.68 %
    Favored  : 90.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.68 (0.47), residues: 99
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.32 (0.36), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARGAB 395 
 TYR   0.023   0.006   TYRAA 372 
 TRP   0.091   0.019   TRPAA 381 
 HIS   0.005   0.003   HISAB 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00536 /  0.27 (  870)
  covalent geometry    : angle       1.07945 /  0.68 ( 1185)
  hydrogen bonds       : bond        0.16095 /  6.98 (    8)
  hydrogen bonds       : angle       6.16291 /  4.18 (   24)

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

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

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.020 
Fit side-chains
REVERT: AC  389 MET cc_start: 0.7229 (mtt) cc_final: 0.7020 (mtt)
REVERT: AC  391 MET cc_start: 0.7390 (mtt) cc_final: 0.6923 (mtp)
REVERT: AA  372 TYR cc_start: 0.6609 (t80) cc_final: 0.6400 (t80)
REVERT: AB  381 TRP cc_start: 0.8198 (p-90) cc_final: 0.6214 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 27
  average time/residue: 0.0680
  time to fit residues: 1.9374
Evaluate side-chains
  13 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 9
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.3985

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
AC 374 ASN
AC 384 ASN
AC 386 HIS
AC 390 HIS
AA 374 ASN
AA 386 HIS
AA 390 HIS
AB 386 HIS
AB 390 HIS
** AB 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.180084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4896 r_free = 0.4896 target = 0.138799 restraints weight = 1732.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4944 r_free = 0.4944 target = 0.141469 restraints weight = 963.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4962 r_free = 0.4962 target = 0.143092 restraints weight = 644.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4982 r_free = 0.4982 target = 0.144264 restraints weight = 484.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4991 r_free = 0.4991 target = 0.144947 restraints weight = 385.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.4639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.4699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027    870  Z= 0.185
  Angle     :  0.803   6.675   1185  Z= 0.458
  Chirality :  0.063   0.185    132
  Planarity :  0.006   0.036    153
  Dihedral  :  7.761  27.955    114
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.17 %
    Favored  : 82.83 %
  Rotamer:
    Outliers :  9.68 %
    Allowed  : 17.20 %
    Favored  : 73.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.67 (0.48), residues: 99
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.32 (0.37), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAC 395 
 TYR   0.019   0.003   TYRAC 372 
 TRP   0.040   0.008   TRPAA 381 
 HIS   0.005   0.003   HISAA 386 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00412 /  0.19 (  870)
  covalent geometry    : angle       0.80270 /  0.46 ( 1185)
  hydrogen bonds       : bond        0.01917 /  0.89 (    8)
  hydrogen bonds       : angle       4.92005 /  3.38 (   24)

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

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

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 16
  time to evaluate  : 0.023 
Fit side-chains
REVERT: AC  377 LEU cc_start: 0.8359 (mt) cc_final: 0.8012 (tt)
REVERT: AC  391 MET cc_start: 0.7304 (mtt) cc_final: 0.6928 (mtp)
REVERT: AA  395 ARG cc_start: 0.7474 (mpp80) cc_final: 0.7191 (mpp80)
REVERT: AB  381 TRP cc_start: 0.7538 (p-90) cc_final: 0.5066 (m100)
  outliers start: 9
  outliers final: 3
  residues processed: 23
  average time/residue: 0.0293
  time to fit residues: 0.7540
Evaluate side-chains
  17 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 14
  time to evaluate  : 0.022 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AC residue  370 ASN
Chi-restraints excluded: chain AA residue  370 ASN
Chi-restraints excluded: chain AB residue  390 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 9
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    0.4980
   chunk 2 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 8 optimal weight:    5.9990
   overall best weight:    0.7733

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
AC 390 HIS
AA 390 HIS
** AA 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
AB 386 HIS
AB 390 HIS
** AB 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4737 r_free = 0.4737 target = 0.185189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4961 r_free = 0.4961 target = 0.143535 restraints weight = 1674.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.5003 r_free = 0.5003 target = 0.146277 restraints weight = 938.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.5034 r_free = 0.5034 target = 0.148180 restraints weight = 626.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.5044 r_free = 0.5044 target = 0.149267 restraints weight = 462.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.5052 r_free = 0.5052 target = 0.150016 restraints weight = 372.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.4704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.5254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017    870  Z= 0.127
  Angle     :  0.698   6.214   1185  Z= 0.390
  Chirality :  0.059   0.168    132
  Planarity :  0.004   0.022    153
  Dihedral  :  6.595  22.156    114
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.11 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  6.45 %
    Allowed  : 19.35 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.13 (0.50), residues: 99
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.90 (0.38), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAB 395 
 TYR   0.011   0.002   TYRAC 372 
 TRP   0.027   0.005   TRPAA 381 
 HIS   0.006   0.001   HISAB 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.13 (  870)
  covalent geometry    : angle       0.69814 /  0.39 ( 1185)
  hydrogen bonds       : bond        0.01266 /  0.73 (    8)
  hydrogen bonds       : angle       4.86047 /  3.33 (   24)

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

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

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 15
  time to evaluate  : 0.021 
Fit side-chains
REVERT: AC  391 MET cc_start: 0.7138 (mtt) cc_final: 0.6732 (mtp)
REVERT: AA  395 ARG cc_start: 0.7500 (mpp80) cc_final: 0.6878 (mtm180)
REVERT: AB  391 MET cc_start: 0.7314 (mtt) cc_final: 0.7080 (mtp)
  outliers start: 6
  outliers final: 3
  residues processed: 21
  average time/residue: 0.0339
  time to fit residues: 0.7890
Evaluate side-chains
  17 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 14
  time to evaluate  : 0.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AC residue  370 ASN
Chi-restraints excluded: chain AA residue  370 ASN
Chi-restraints excluded: chain AB residue  390 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 9
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0980
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.2235

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
AC 390 HIS
AA 374 ASN
AA 384 ASN
** AA 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
AB 384 ASN
AB 386 HIS
AB 390 HIS
** AB 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.180687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4900 r_free = 0.4900 target = 0.137079 restraints weight = 1703.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4959 r_free = 0.4959 target = 0.139729 restraints weight = 920.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4969 r_free = 0.4969 target = 0.141211 restraints weight = 589.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4982 r_free = 0.4982 target = 0.142247 restraints weight = 441.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4993 r_free = 0.4993 target = 0.142986 restraints weight = 361.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.4617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.5836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025    870  Z= 0.157
  Angle     :  0.819   8.612   1185  Z= 0.435
  Chirality :  0.062   0.193    132
  Planarity :  0.004   0.014    153
  Dihedral  :  6.998  23.890    114
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.19 %
    Favored  : 80.81 %
  Rotamer:
    Outliers :  8.60 %
    Allowed  : 22.58 %
    Favored  : 68.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.02 (0.51), residues: 99
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.82 (0.39), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAB 395 
 TYR   0.016   0.003   TYRAC 372 
 TRP   0.030   0.004   TRPAA 381 
 HIS   0.006   0.001   HISAB 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.16 (  870)
  covalent geometry    : angle       0.81856 /  0.44 ( 1185)
  hydrogen bonds       : bond        0.01199 /  0.70 (    8)
  hydrogen bonds       : angle       4.75994 /  3.30 (   24)

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

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

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 15
  time to evaluate  : 0.030 
Fit side-chains
REVERT: AC  381 TRP cc_start: 0.8448 (OUTLIER) cc_final: 0.8215 (p-90)
REVERT: AC  390 HIS cc_start: 0.7822 (OUTLIER) cc_final: 0.7561 (m-70)
REVERT: AC  391 MET cc_start: 0.7107 (mtt) cc_final: 0.6658 (mtp)
REVERT: AA  389 MET cc_start: 0.7512 (mtt) cc_final: 0.7163 (ttt)
REVERT: AA  395 ARG cc_start: 0.7423 (mpp80) cc_final: 0.6766 (mtm180)
REVERT: AB  381 TRP cc_start: 0.7361 (p-90) cc_final: 0.4955 (m100)
  outliers start: 8
  outliers final: 4
  residues processed: 21
  average time/residue: 0.0317
  time to fit residues: 0.7540
Evaluate side-chains
  21 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 15
  time to evaluate  : 0.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AC residue  370 ASN
Chi-restraints excluded: chain AC residue  381 TRP
Chi-restraints excluded: chain AC residue  390 HIS
Chi-restraints excluded: chain AA residue  370 ASN
Chi-restraints excluded: chain AB residue  370 ASN
Chi-restraints excluded: chain AB residue  390 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 9
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0980
   chunk 7 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.5480

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
AC 390 HIS
** AA 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
AB 386 HIS
AB 390 HIS
** AB 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4722 r_free = 0.4722 target = 0.191176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.5009 r_free = 0.5009 target = 0.146409 restraints weight = 1728.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.5059 r_free = 0.5059 target = 0.149261 restraints weight = 949.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.5073 r_free = 0.5073 target = 0.151026 restraints weight = 614.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.5089 r_free = 0.5089 target = 0.152302 restraints weight = 451.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.5110 r_free = 0.5110 target = 0.153227 restraints weight = 357.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.4689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.6151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015    870  Z= 0.118
  Angle     :  0.729   7.631   1185  Z= 0.385
  Chirality :  0.060   0.188    132
  Planarity :  0.003   0.009    153
  Dihedral  :  6.191  18.693    114
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.11 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 23.66 %
    Favored  : 70.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.68 (0.53), residues: 99
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.56 (0.41), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAA 395 
 TYR   0.009   0.002   TYRAA 372 
 TRP   0.024   0.003   TRPAA 381 
 HIS   0.003   0.001   HISAB 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.12 (  870)
  covalent geometry    : angle       0.72888 /  0.38 ( 1185)
  hydrogen bonds       : bond        0.01192 /  0.60 (    8)
  hydrogen bonds       : angle       4.87875 /  3.27 (   24)

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

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

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 15
  time to evaluate  : 0.035 
Fit side-chains
REVERT: AC  391 MET cc_start: 0.6989 (mtt) cc_final: 0.6520 (mtp)
REVERT: AA  381 TRP cc_start: 0.8006 (OUTLIER) cc_final: 0.6908 (p-90)
REVERT: AA  389 MET cc_start: 0.7362 (mtt) cc_final: 0.7150 (ttt)
REVERT: AA  395 ARG cc_start: 0.7413 (mpp80) cc_final: 0.6794 (mtm180)
  outliers start: 5
  outliers final: 1
  residues processed: 19
  average time/residue: 0.0553
  time to fit residues: 1.1648
Evaluate side-chains
  16 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AA residue  381 TRP
Chi-restraints excluded: chain AB residue  390 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 9
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0040
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.8748

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
AC 390 HIS
** AA 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
AB 386 HIS
AB 390 HIS
** AB 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4704 r_free = 0.4704 target = 0.190019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.5000 r_free = 0.5000 target = 0.144922 restraints weight = 1735.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.5039 r_free = 0.5039 target = 0.147605 restraints weight = 909.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.5063 r_free = 0.5063 target = 0.149350 restraints weight = 582.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.5072 r_free = 0.5072 target = 0.150420 restraints weight = 419.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.5079 r_free = 0.5079 target = 0.151209 restraints weight = 338.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.4674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.6487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021    870  Z= 0.133
  Angle     :  0.747   7.840   1185  Z= 0.401
  Chirality :  0.060   0.179    132
  Planarity :  0.003   0.012    153
  Dihedral  :  6.248  20.663    114
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.18 %
    Favored  : 81.82 %
  Rotamer:
    Outliers :  6.45 %
    Allowed  : 20.43 %
    Favored  : 73.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.71 (0.55), residues: 99
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.59 (0.42), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAA 395 
 TYR   0.012   0.002   TYRAA 372 
 TRP   0.032   0.004   TRPAA 381 
 HIS   0.007   0.001   HISAB 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 (  870)
  covalent geometry    : angle       0.74679 /  0.40 ( 1185)
  hydrogen bonds       : bond        0.01042 /  0.66 (    8)
  hydrogen bonds       : angle       4.78083 /  3.25 (   24)

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

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

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 15
  time to evaluate  : 0.034 
Fit side-chains
REVERT: AC  381 TRP cc_start: 0.8314 (OUTLIER) cc_final: 0.6892 (p-90)
REVERT: AC  391 MET cc_start: 0.6881 (mtt) cc_final: 0.6442 (mtp)
REVERT: AA  381 TRP cc_start: 0.7900 (OUTLIER) cc_final: 0.6897 (p-90)
REVERT: AA  389 MET cc_start: 0.7385 (mtt) cc_final: 0.7153 (ttt)
REVERT: AA  395 ARG cc_start: 0.7329 (mpp80) cc_final: 0.6724 (mtm180)
  outliers start: 6
  outliers final: 2
  residues processed: 20
  average time/residue: 0.0522
  time to fit residues: 1.1506
Evaluate side-chains
  19 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 15
  time to evaluate  : 0.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AC residue  381 TRP
Chi-restraints excluded: chain AA residue  370 ASN
Chi-restraints excluded: chain AA residue  381 TRP
Chi-restraints excluded: chain AB residue  390 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 9
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0970
   chunk 7 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.9733

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
AC 390 HIS
** AA 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
AB 386 HIS
AB 390 HIS
** AB 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.125602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.110281 restraints weight = 1750.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.112898 restraints weight = 952.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.114758 restraints weight = 637.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.116013 restraints weight = 475.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.117041 restraints weight = 383.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.4526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7171
moved from start:          0.6723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022    870  Z= 0.138
  Angle     :  0.752   7.728   1185  Z= 0.407
  Chirality :  0.060   0.179    132
  Planarity :  0.003   0.012    153
  Dihedral  :  6.353  21.101    114
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.18 %
    Favored  : 81.82 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 21.51 %
    Favored  : 73.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.75 (0.54), residues: 99
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.61 (0.41), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAB 395 
 TYR   0.013   0.002   TYRAC 372 
 TRP   0.032   0.004   TRPAA 381 
 HIS   0.006   0.001   HISAB 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.14 (  870)
  covalent geometry    : angle       0.75166 /  0.41 ( 1185)
  hydrogen bonds       : bond        0.01281 /  0.81 (    8)
  hydrogen bonds       : angle       4.70995 /  3.23 (   24)

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

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

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 15
  time to evaluate  : 0.037 
Fit side-chains
REVERT: AC  381 TRP cc_start: 0.8221 (p-90) cc_final: 0.6582 (p-90)
REVERT: AC  391 MET cc_start: 0.6855 (mtt) cc_final: 0.6408 (mtp)
REVERT: AA  381 TRP cc_start: 0.7818 (OUTLIER) cc_final: 0.6854 (p-90)
REVERT: AA  389 MET cc_start: 0.7426 (mtt) cc_final: 0.7137 (ttt)
REVERT: AA  395 ARG cc_start: 0.7443 (mpp80) cc_final: 0.7118 (mpp80)
  outliers start: 5
  outliers final: 2
  residues processed: 20
  average time/residue: 0.0547
  time to fit residues: 1.2207
Evaluate side-chains
  18 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 15
  time to evaluate  : 0.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AA residue  370 ASN
Chi-restraints excluded: chain AA residue  381 TRP
Chi-restraints excluded: chain AB residue  390 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 9
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.9983

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
AC 390 HIS
** AA 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
AB 386 HIS
AB 390 HIS
** AB 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4609 r_free = 0.4609 target = 0.124999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.109574 restraints weight = 1806.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.112272 restraints weight = 975.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.114064 restraints weight = 650.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.115288 restraints weight = 486.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.116271 restraints weight = 393.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.4516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.6935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022    870  Z= 0.138
  Angle     :  0.747   7.366   1185  Z= 0.407
  Chirality :  0.060   0.168    132
  Planarity :  0.003   0.012    153
  Dihedral  :  6.345  21.001    114
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.19 %
    Favored  : 80.81 %
  Rotamer:
    Outliers :  7.53 %
    Allowed  : 19.35 %
    Favored  : 73.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.80 (0.54), residues: 99
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.65 (0.41), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAA 395 
 TYR   0.013   0.002   TYRAC 372 
 TRP   0.032   0.004   TRPAA 381 
 HIS   0.004   0.001   HISAB 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.14 (  870)
  covalent geometry    : angle       0.74659 /  0.41 ( 1185)
  hydrogen bonds       : bond        0.01459 /  0.86 (    8)
  hydrogen bonds       : angle       4.74126 /  3.31 (   24)

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

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

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 14
  time to evaluate  : 0.035 
Fit side-chains
REVERT: AC  381 TRP cc_start: 0.7832 (p-90) cc_final: 0.6417 (p-90)
REVERT: AC  391 MET cc_start: 0.6933 (mtt) cc_final: 0.6467 (mtp)
REVERT: AA  381 TRP cc_start: 0.7898 (OUTLIER) cc_final: 0.6956 (p-90)
REVERT: AA  389 MET cc_start: 0.7450 (mtt) cc_final: 0.7168 (ttt)
  outliers start: 7
  outliers final: 4
  residues processed: 21
  average time/residue: 0.0292
  time to fit residues: 0.7430
Evaluate side-chains
  19 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 14
  time to evaluate  : 0.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AC residue  370 ASN
Chi-restraints excluded: chain AA residue  370 ASN
Chi-restraints excluded: chain AA residue  381 TRP
Chi-restraints excluded: chain AB residue  370 ASN
Chi-restraints excluded: chain AB residue  390 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 9
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 2 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.6988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
AC 390 HIS
AA 374 ASN
** AA 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
AB 386 HIS
AB 390 HIS
** AB 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.185598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4916 r_free = 0.4916 target = 0.137071 restraints weight = 1739.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4953 r_free = 0.4953 target = 0.139610 restraints weight = 863.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4977 r_free = 0.4977 target = 0.141198 restraints weight = 538.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4987 r_free = 0.4987 target = 0.142121 restraints weight = 385.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4993 r_free = 0.4993 target = 0.142671 restraints weight = 309.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.4574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.7147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032    870  Z= 0.197
  Angle     :  0.837   7.122   1185  Z= 0.464
  Chirality :  0.063   0.177    132
  Planarity :  0.004   0.015    153
  Dihedral  :  7.213  25.271    114
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 23.23 %
    Favored  : 76.77 %
  Rotamer:
    Outliers :  8.60 %
    Allowed  : 21.51 %
    Favored  : 69.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.88 (0.53), residues: 99
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.71 (0.40), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAB 395 
 TYR   0.020   0.004   TYRAC 372 
 TRP   0.038   0.005   TRPAA 381 
 HIS   0.011   0.003   HISAB 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00440 /  0.20 (  870)
  covalent geometry    : angle       0.83715 /  0.46 ( 1185)
  hydrogen bonds       : bond        0.01440 /  0.81 (    8)
  hydrogen bonds       : angle       4.77965 /  3.35 (   24)

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

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

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 17
  time to evaluate  : 0.037 
Fit side-chains
REVERT: AC  381 TRP cc_start: 0.7772 (p-90) cc_final: 0.6316 (p-90)
REVERT: AC  391 MET cc_start: 0.7003 (mtt) cc_final: 0.6534 (mtp)
REVERT: AA  381 TRP cc_start: 0.8322 (OUTLIER) cc_final: 0.7261 (p-90)
REVERT: AB  381 TRP cc_start: 0.7864 (p-90) cc_final: 0.4943 (m100)
  outliers start: 8
  outliers final: 4
  residues processed: 24
  average time/residue: 0.0471
  time to fit residues: 1.2675
Evaluate side-chains
  22 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 17
  time to evaluate  : 0.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AC residue  370 ASN
Chi-restraints excluded: chain AA residue  370 ASN
Chi-restraints excluded: chain AA residue  381 TRP
Chi-restraints excluded: chain AB residue  370 ASN
Chi-restraints excluded: chain AB residue  390 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 9
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 4 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
AC 390 HIS
AA 393 GLN
** AA 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
AB 386 HIS
AB 390 HIS
** AB 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.194743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.5000 r_free = 0.5000 target = 0.144113 restraints weight = 1667.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.5032 r_free = 0.5032 target = 0.146962 restraints weight = 842.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.5055 r_free = 0.5055 target = 0.148748 restraints weight = 526.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.5066 r_free = 0.5066 target = 0.149819 restraints weight = 373.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.5074 r_free = 0.5074 target = 0.150626 restraints weight = 294.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.4662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.7469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019    870  Z= 0.121
  Angle     :  0.724   7.344   1185  Z= 0.393
  Chirality :  0.059   0.163    132
  Planarity :  0.003   0.012    153
  Dihedral  :  6.231  19.781    114
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.11 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 26.88 %
    Favored  : 69.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.75 (0.52), residues: 99
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.62 (0.40), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAA 395 
 TYR   0.010   0.002   TYRAB 372 
 TRP   0.029   0.003   TRPAA 381 
 HIS   0.005   0.001   HISAB 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 (  870)
  covalent geometry    : angle       0.72402 /  0.39 ( 1185)
  hydrogen bonds       : bond        0.01358 /  0.74 (    8)
  hydrogen bonds       : angle       4.57967 /  3.09 (   24)

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

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

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  198 Ramachandran restraints generated.
    99 Oldfield, 0 Emsley, 99 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 15
  time to evaluate  : 0.040 
Fit side-chains
REVERT: AC  381 TRP cc_start: 0.7594 (p-90) cc_final: 0.6244 (p-90)
REVERT: AC  391 MET cc_start: 0.6958 (mtt) cc_final: 0.6547 (mtp)
REVERT: AA  381 TRP cc_start: 0.8123 (OUTLIER) cc_final: 0.6942 (p-90)
REVERT: AB  386 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.7022 (t-90)
  outliers start: 3
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0578
  time to fit residues: 1.1626
Evaluate side-chains
  17 residues out of total 93 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 15
  time to evaluate  : 0.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain AA residue  381 TRP
Chi-restraints excluded: chain AB residue  386 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 9
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
AC 390 HIS
AA 374 ASN
** AA 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
AB 386 HIS
** AB 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.193026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4986 r_free = 0.4986 target = 0.145440 restraints weight = 1718.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.5009 r_free = 0.5009 target = 0.147863 restraints weight = 850.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.5037 r_free = 0.5037 target = 0.149812 restraints weight = 551.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.5050 r_free = 0.5050 target = 0.151012 restraints weight = 388.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.5055 r_free = 0.5055 target = 0.151375 restraints weight = 297.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.4665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.7455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020    870  Z= 0.126
  Angle     :  0.723   7.202   1185  Z= 0.392
  Chirality :  0.059   0.162    132
  Planarity :  0.003   0.012    153
  Dihedral  :  6.071  19.573    114
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.20 %
    Favored  : 79.80 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 23.66 %
    Favored  : 70.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.79 (0.52), residues: 99
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.65 (0.40), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARGAA 395 
 TYR   0.011   0.002   TYRAA 372 
 TRP   0.029   0.004   TRPAA 381 
 HIS   0.005   0.001   HISAB 386 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.13 (  870)
  covalent geometry    : angle       0.72294 /  0.39 ( 1185)
  hydrogen bonds       : bond        0.01391 /  0.83 (    8)
  hydrogen bonds       : angle       4.43074 /  2.96 (   24)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 444.55 seconds
wall clock time: 8 minutes 37.62 seconds (517.62 seconds total)