Starting phenix.real_space_refine
on Fri May  9 13:21:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x5x_38074/05_2025/8x5x_38074.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x5x_38074/05_2025/8x5x_38074.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x5x_38074/05_2025/8x5x_38074.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x5x_38074/05_2025/8x5x_38074.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x5x_38074/05_2025/8x5x_38074.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x5x_38074/05_2025/8x5x_38074.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.052
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    1410      2.51       5
     N     339      2.21       5
     O     337      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 2105
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 2105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 2105
          Classifications: {'peptide': 256}
          Link IDs: {'PTRANS': 8, 'TRANS': 247}
          Chain breaks: 4
  Time building chain proxies: 2.08, per 1000 atoms: 0.99
  Number of scatterers: 2105
  At special positions: 0
  Unit cell: (49.22, 70.62, 72.76, 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     337      8.00
     N     339      7.00
     C    1410      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 100 " - pdb=" SG  CYS B 180 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 441 " - pdb=" SG  CYS B 444 " distance=2.03

  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: 0.53
  Conformation dependent library (CDL) restraints added in 239.1 milliseconds
  

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  496

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 0 sheets defined
      85.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'B' and resid 29 through 55
      removed outlier: 3.861A  pdb=" N   VAL B  33 " --> pdb=" O   PRO B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 90
      Proline residue:  B  82  - end of helix
      removed outlier: 4.414A  pdb=" N   MET B  90 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 131
    Processing helix  chain 'B' and resid 132 through 134
      No H-bonds generated for 'chain 'B' and resid 132 through 134'
    Processing helix  chain 'B' and resid 140 through 157
      removed outlier: 3.887A  pdb=" N   SER B 145 " --> pdb=" O   LYS B 141 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   ALA B 146 " --> pdb=" O   THR B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 164
      removed outlier: 3.932A  pdb=" N   ILE B 162 " --> pdb=" O   TRP B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 221
      removed outlier: 5.167A  pdb=" N   LEU B 201 " --> pdb=" O   ILE B 197 " (cutoff:3.500A)
      Proline residue:  B 202  - end of helix
    Processing helix  chain 'B' and resid 409 through 439
      Proline residue:  B 430  - end of helix
    Processing helix  chain 'B' and resid 446 through 472
      Proline residue:  B 465  - end of helix
      Proline residue:  B 469  - end of helix
      removed outlier: 3.797A  pdb=" N   ASN B 472 " --> pdb=" O   TYR B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 472 through 481
      removed outlier: 3.700A  pdb=" N   ARG B 481 " --> pdb=" O   LYS B 477 " (cutoff:3.500A)

    157 hydrogen bonds defined for protein.
    471 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: 0.49

  Time building geometry restraints manager: 0.61 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 608
        1.35 -     1.47: 608
        1.47 -     1.60: 917
        1.60 -     1.72: 0
        1.72 -     1.84: 29
  Bond restraints: 2162
  Sorted by residual:
  bond pdb=" C   ILE B 429 "
       pdb=" N   PRO B 430 "
    ideal  model  delta    sigma   weight residual
    1.334  1.379 -0.045 2.34e-02 1.83e+03 3.68e+00
  bond pdb=" CG1 ILE B 438 "
       pdb=" CD1 ILE B 438 "
    ideal  model  delta    sigma   weight residual
    1.513  1.456  0.057 3.90e-02 6.57e+02 2.13e+00
  bond pdb=" CG1 ILE B 115 "
       pdb=" CD1 ILE B 115 "
    ideal  model  delta    sigma   weight residual
    1.513  1.459  0.054 3.90e-02 6.57e+02 1.91e+00
  bond pdb=" CB  CYS B 180 "
       pdb=" SG  CYS B 180 "
    ideal  model  delta    sigma   weight residual
    1.808  1.843 -0.035 3.30e-02 9.18e+02 1.15e+00
  bond pdb=" N   GLU B 181 "
       pdb=" CA  GLU B 181 "
    ideal  model  delta    sigma   weight residual
    1.468  1.455  0.013 1.24e-02 6.50e+03 1.12e+00
  ... (remaining 2157 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 2797
        1.60 -     3.19: 101
        3.19 -     4.79: 23
        4.79 -     6.38: 10
        6.38 -     7.98: 2
  Bond angle restraints: 2933
  Sorted by residual:
  angle pdb=" CA  TRP B 455 "
        pdb=" CB  TRP B 455 "
        pdb=" CG  TRP B 455 "
      ideal   model   delta    sigma   weight residual
     113.60  118.52   -4.92 1.90e+00 2.77e-01 6.69e+00
  angle pdb=" CA  LEU B  39 "
        pdb=" CB  LEU B  39 "
        pdb=" CG  LEU B  39 "
      ideal   model   delta    sigma   weight residual
     116.30  124.28   -7.98 3.50e+00 8.16e-02 5.20e+00
  angle pdb=" C   THR B 478 "
        pdb=" N   PHE B 479 "
        pdb=" CA  PHE B 479 "
      ideal   model   delta    sigma   weight residual
     121.58  117.23    4.35 1.95e+00 2.63e-01 4.97e+00
  angle pdb=" C   LEU B 426 "
        pdb=" N   CYS B 427 "
        pdb=" CA  CYS B 427 "
      ideal   model   delta    sigma   weight residual
     122.65  119.13    3.52 1.60e+00 3.91e-01 4.85e+00
  angle pdb=" N   GLY B  96 "
        pdb=" CA  GLY B  96 "
        pdb=" C   GLY B  96 "
      ideal   model   delta    sigma   weight residual
     113.18  108.34    4.84 2.37e+00 1.78e-01 4.16e+00
  ... (remaining 2928 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.23: 1104
       16.23 -    32.46: 119
       32.46 -    48.69: 34
       48.69 -    64.91: 3
       64.91 -    81.14: 3
  Dihedral angle restraints: 1263
    sinusoidal: 504
      harmonic: 759
  Sorted by residual:
  dihedral pdb=" CB  CYS B 441 "
           pdb=" SG  CYS B 441 "
           pdb=" SG  CYS B 444 "
           pdb=" CB  CYS B 444 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  174.14  -81.14     1      1.00e+01 1.00e-02 8.12e+01
  dihedral pdb=" SG  CYS B 441 "
           pdb=" CB  CYS B 444 "
           pdb=" SG  CYS B 444 "
           pdb=" CA  CYS B 444 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00    8.82   70.18     1      2.00e+01 2.50e-03 1.59e+01
  dihedral pdb=" CA  CYS B 427 "
           pdb=" C   CYS B 427 "
           pdb=" N   TRP B 428 "
           pdb=" CA  TRP B 428 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.55   18.45     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 1260 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 208
       0.032 -    0.065: 84
       0.065 -    0.097: 36
       0.097 -    0.129: 10
       0.129 -    0.162: 2
  Chirality restraints: 340
  Sorted by residual:
  chirality pdb=" CG  LEU B  74 "
            pdb=" CB  LEU B  74 "
            pdb=" CD1 LEU B  74 "
            pdb=" CD2 LEU B  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.54e-01
  chirality pdb=" CB  VAL B  79 "
            pdb=" CA  VAL B  79 "
            pdb=" CG1 VAL B  79 "
            pdb=" CG2 VAL B  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.53e-01
  chirality pdb=" CA  ILE B 115 "
            pdb=" N   ILE B 115 "
            pdb=" C   ILE B 115 "
            pdb=" CB  ILE B 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.94e-01
  ... (remaining 337 not shown)

  Planarity restraints: 344
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 455 "   -0.020 2.00e-02 2.50e+03   1.56e-02 6.06e+00
        pdb=" CG  TRP B 455 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 455 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 455 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 455 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 455 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 455 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 455 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 455 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 455 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 428 "    0.016 2.00e-02 2.50e+03   1.25e-02 3.88e+00
        pdb=" CG  TRP B 428 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 428 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 428 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 428 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 428 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 428 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 428 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 428 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 428 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 479 "    0.013 2.00e-02 2.50e+03   1.33e-02 3.09e+00
        pdb=" CG  PHE B 479 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 479 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 479 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 479 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 479 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 479 "    0.000 2.00e-02 2.50e+03
  ... (remaining 341 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.66: 18
        2.66 -     3.22: 2097
        3.22 -     3.78: 3431
        3.78 -     4.34: 4203
        4.34 -     4.90: 6642
  Nonbonded interactions: 16391
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B  63 "
            pdb=" OH  TYR B 468 "
     model   vdw
     2.094 3.040
  nonbonded pdb=" OH  TYR B  65 "
            pdb=" OG1 THR B 147 "
     model   vdw
     2.143 3.040
  nonbonded pdb=" OG1 THR B  41 "
            pdb=" OG1 THR B 462 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   TYR B 458 "
            pdb=" OG  SER B 461 "
     model   vdw
     2.364 3.040
  nonbonded pdb=" ND2 ASN B  45 "
            pdb=" OD2 ASP B  73 "
     model   vdw
     2.406 3.120
  ... (remaining 16386 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=0.00 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:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.340
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5295
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      :  0.004   0.057   2164  Z= 0.165
  Angle     :  0.779   7.979   2937  Z= 0.394
  Chirality :  0.044   0.162    340
  Planarity :  0.005   0.037    344
  Dihedral  : 14.147  79.862    761
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 14.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  0.43 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.56), residues: 246
  helix:  1.40 (0.37), residues: 200
  sheet:  None (None), residues: 0
  loop : -2.56 (0.94), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP B 455 
 HIS   0.003   0.001   HIS B 450 
 PHE   0.031   0.002   PHE B 479 
 TYR   0.014   0.002   TYR B 185 
 ARG   0.002   0.000   ARG B  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07067 (  157)
  hydrogen bonds       : angle       4.57808 (  471)
  SS BOND              : bond        0.00523 (    2)
  SS BOND              : angle       2.32916 (    4)
  covalent geometry    : bond        0.00376 ( 2162)
  covalent geometry    : angle       0.77451 ( 2933)

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.238 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1207
  time to fit residues: 7.8008
Evaluate side-chains
  41 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 21 optimal weight:    0.0070
   chunk 18 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0970
   chunk 22 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
B  84 ASN
** B 460 ASN ** 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 = 0.4642 r_free = 0.4642 target = 0.191664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.178713 restraints weight = 4889.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.181744 restraints weight = 2863.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.183700 restraints weight = 1893.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.4560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5408
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   2164  Z= 0.142
  Angle     :  0.729   7.601   2937  Z= 0.353
  Chirality :  0.042   0.135    340
  Planarity :  0.004   0.043    344
  Dihedral  :  4.942  18.212    275
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 10.78 %
    Favored  : 87.50 %
  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:  1.01 (0.55), residues: 246
  helix:  1.37 (0.36), residues: 201
  sheet:  None (None), residues: 0
  loop : -2.54 (0.96), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 455 
 HIS   0.002   0.001   HIS B  59 
 PHE   0.025   0.002   PHE B 479 
 TYR   0.012   0.002   TYR B 126 
 ARG   0.001   0.000   ARG B  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03623 (  157)
  hydrogen bonds       : angle       4.19004 (  471)
  SS BOND              : bond        0.00447 (    2)
  SS BOND              : angle       2.47493 (    4)
  covalent geometry    : bond        0.00321 ( 2162)
  covalent geometry    : angle       0.72383 ( 2933)

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: B  185 TYR cc_start: 0.2817 (m-10) cc_final: 0.2474 (m-80)
REVERT: B  461 SER cc_start: 0.7874 (p) cc_final: 0.7602 (t)
  outliers start: 4
  outliers final: 4
  residues processed: 47
  average time/residue: 0.0914
  time to fit residues: 5.5251
Evaluate side-chains
  42 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  197 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 7 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 464 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.186821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.173692 restraints weight = 4795.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.176607 restraints weight = 2821.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.178626 restraints weight = 1878.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.4499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5674
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   2164  Z= 0.183
  Angle     :  0.762   8.156   2937  Z= 0.381
  Chirality :  0.044   0.129    340
  Planarity :  0.005   0.048    344
  Dihedral  :  4.950  15.389    275
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 15.95 %
    Favored  : 79.31 %
  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:  0.91 (0.53), residues: 246
  helix:  1.26 (0.36), residues: 201
  sheet:  None (None), residues: 0
  loop : -2.35 (0.86), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 455 
 HIS   0.010   0.002   HIS B 167 
 PHE   0.024   0.002   PHE B 479 
 TYR   0.014   0.002   TYR B 431 
 ARG   0.002   0.000   ARG B 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04233 (  157)
  hydrogen bonds       : angle       4.39215 (  471)
  SS BOND              : bond        0.00456 (    2)
  SS BOND              : angle       2.39372 (    4)
  covalent geometry    : bond        0.00419 ( 2162)
  covalent geometry    : angle       0.75770 ( 2933)

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: B  126 TYR cc_start: 0.5398 (OUTLIER) cc_final: 0.5096 (t80)
  outliers start: 11
  outliers final: 8
  residues processed: 45
  average time/residue: 0.0972
  time to fit residues: 5.5873
Evaluate side-chains
  41 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   90 MET
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  126 TYR
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  204 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 3 optimal weight:    0.1980
   chunk 5 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0070
   chunk 13 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
B  45 ASN
** B 460 ASN ** 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 = 0.4651 r_free = 0.4651 target = 0.191112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.178269 restraints weight = 4845.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.181267 restraints weight = 2812.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.183231 restraints weight = 1866.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.4560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5569
moved from start:          0.3435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   2164  Z= 0.140
  Angle     :  0.717   7.470   2937  Z= 0.348
  Chirality :  0.041   0.122    340
  Planarity :  0.005   0.051    344
  Dihedral  :  4.707  15.902    275
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 20.26 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.89 (0.54), residues: 246
  helix:  1.23 (0.36), residues: 201
  sheet:  None (None), residues: 0
  loop : -2.26 (0.87), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 455 
 HIS   0.002   0.001   HIS B  59 
 PHE   0.029   0.002   PHE B 479 
 TYR   0.009   0.001   TYR B 126 
 ARG   0.001   0.000   ARG B  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03853 (  157)
  hydrogen bonds       : angle       4.26459 (  471)
  SS BOND              : bond        0.00351 (    2)
  SS BOND              : angle       2.18478 (    4)
  covalent geometry    : bond        0.00315 ( 2162)
  covalent geometry    : angle       0.71292 ( 2933)

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 38
  time to evaluate  : 0.226 
Fit side-chains
REVERT: B  165 TRP cc_start: 0.5199 (t-100) cc_final: 0.4304 (t-100)
  outliers start: 11
  outliers final: 5
  residues processed: 44
  average time/residue: 0.0843
  time to fit residues: 4.7799
Evaluate side-chains
  41 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  204 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 2 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.187122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.173704 restraints weight = 4809.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.176757 restraints weight = 2778.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.178918 restraints weight = 1853.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.4527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5636
moved from start:          0.3701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   2164  Z= 0.145
  Angle     :  0.695   7.569   2937  Z= 0.341
  Chirality :  0.041   0.130    340
  Planarity :  0.005   0.048    344
  Dihedral  :  4.750  16.347    275
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 22.41 %
    Favored  : 73.28 %
  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:  1.06 (0.54), residues: 246
  helix:  1.38 (0.37), residues: 201
  sheet:  None (None), residues: 0
  loop : -2.41 (0.83), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 455 
 HIS   0.002   0.001   HIS B 167 
 PHE   0.025   0.002   PHE B 479 
 TYR   0.009   0.001   TYR B 468 
 ARG   0.001   0.000   ARG B  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03850 (  157)
  hydrogen bonds       : angle       4.28462 (  471)
  SS BOND              : bond        0.00418 (    2)
  SS BOND              : angle       2.10342 (    4)
  covalent geometry    : bond        0.00327 ( 2162)
  covalent geometry    : angle       0.69085 ( 2933)

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 0.239 
Fit side-chains
REVERT: B   93 TRP cc_start: 0.5178 (OUTLIER) cc_final: 0.4413 (m-10)
REVERT: B  165 TRP cc_start: 0.5139 (t-100) cc_final: 0.4205 (t-100)
REVERT: B  450 HIS cc_start: 0.6711 (OUTLIER) cc_final: 0.6055 (t-90)
  outliers start: 10
  outliers final: 6
  residues processed: 40
  average time/residue: 0.0906
  time to fit residues: 4.7139
Evaluate side-chains
  40 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   93 TRP
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  450 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0980
   chunk 15 optimal weight:    0.8980
   chunk 2 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.188188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4470 r_free = 0.4470 target = 0.175799 restraints weight = 5030.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.178675 restraints weight = 3006.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.180670 restraints weight = 2041.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.4532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5623
moved from start:          0.4048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   2164  Z= 0.135
  Angle     :  0.678   7.371   2937  Z= 0.327
  Chirality :  0.040   0.120    340
  Planarity :  0.004   0.048    344
  Dihedral  :  4.610  16.715    275
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 22.41 %
    Favored  : 71.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.54), residues: 246
  helix:  1.43 (0.37), residues: 201
  sheet:  None (None), residues: 0
  loop : -2.20 (0.88), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 455 
 HIS   0.002   0.001   HIS B 167 
 PHE   0.025   0.002   PHE B 479 
 TYR   0.007   0.001   TYR B 126 
 ARG   0.001   0.000   ARG B  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03753 (  157)
  hydrogen bonds       : angle       4.17300 (  471)
  SS BOND              : bond        0.00331 (    2)
  SS BOND              : angle       2.15427 (    4)
  covalent geometry    : bond        0.00301 ( 2162)
  covalent geometry    : angle       0.67409 ( 2933)

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 35
  time to evaluate  : 0.186 
Fit side-chains
REVERT: B   93 TRP cc_start: 0.5360 (OUTLIER) cc_final: 0.5061 (m-10)
REVERT: B  101 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7106 (mt)
REVERT: B  126 TYR cc_start: 0.5300 (OUTLIER) cc_final: 0.4863 (t80)
REVERT: B  165 TRP cc_start: 0.5129 (t-100) cc_final: 0.4262 (t-100)
REVERT: B  450 HIS cc_start: 0.6545 (OUTLIER) cc_final: 0.6032 (t-90)
  outliers start: 13
  outliers final: 7
  residues processed: 46
  average time/residue: 0.0846
  time to fit residues: 4.9877
Evaluate side-chains
  42 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 31
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   93 TRP
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  126 TYR
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  450 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0170
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
B 130 GLN
** B 460 ASN ** 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 = 0.4605 r_free = 0.4605 target = 0.187283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.174453 restraints weight = 5066.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.177472 restraints weight = 2960.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.179646 restraints weight = 1978.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.4520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5641
moved from start:          0.4278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   2164  Z= 0.139
  Angle     :  0.727   8.321   2937  Z= 0.350
  Chirality :  0.040   0.148    340
  Planarity :  0.004   0.048    344
  Dihedral  :  5.160  40.411    275
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 22.41 %
    Favored  : 72.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.41 %

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:  1.17 (0.54), residues: 246
  helix:  1.55 (0.37), residues: 200
  sheet:  None (None), residues: 0
  loop : -2.75 (0.79), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 455 
 HIS   0.002   0.001   HIS B 167 
 PHE   0.023   0.001   PHE B 479 
 TYR   0.007   0.001   TYR B 126 
 ARG   0.001   0.000   ARG B  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03870 (  157)
  hydrogen bonds       : angle       4.16705 (  471)
  SS BOND              : bond        0.00585 (    2)
  SS BOND              : angle       4.66968 (    4)
  covalent geometry    : bond        0.00318 ( 2162)
  covalent geometry    : angle       0.70715 ( 2933)

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 33
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: B  126 TYR cc_start: 0.5309 (OUTLIER) cc_final: 0.4823 (t80)
REVERT: B  165 TRP cc_start: 0.5175 (t-100) cc_final: 0.4350 (t-100)
REVERT: B  450 HIS cc_start: 0.6551 (OUTLIER) cc_final: 0.5991 (t-90)
  outliers start: 12
  outliers final: 9
  residues processed: 42
  average time/residue: 0.1014
  time to fit residues: 5.3609
Evaluate side-chains
  43 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   93 TRP
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  126 TYR
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  435 PHE
Chi-restraints excluded: chain B residue  450 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 13 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0570
   chunk 23 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.185600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.172563 restraints weight = 5119.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.175654 restraints weight = 2895.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.177710 restraints weight = 1894.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.4501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5647
moved from start:          0.4448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   2164  Z= 0.143
  Angle     :  0.744   7.330   2937  Z= 0.357
  Chirality :  0.040   0.117    340
  Planarity :  0.004   0.048    344
  Dihedral  :  5.202  38.315    275
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 24.57 %
    Favored  : 71.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.41 %

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:  1.10 (0.54), residues: 246
  helix:  1.46 (0.37), residues: 200
  sheet:  None (None), residues: 0
  loop : -2.57 (0.83), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 455 
 HIS   0.002   0.001   HIS B 167 
 PHE   0.023   0.001   PHE B 479 
 TYR   0.008   0.001   TYR B 468 
 ARG   0.001   0.000   ARG B  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03893 (  157)
  hydrogen bonds       : angle       4.18893 (  471)
  SS BOND              : bond        0.00315 (    2)
  SS BOND              : angle       3.68466 (    4)
  covalent geometry    : bond        0.00328 ( 2162)
  covalent geometry    : angle       0.73227 ( 2933)

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 34
  time to evaluate  : 0.215 
Fit side-chains
REVERT: B   93 TRP cc_start: 0.5215 (OUTLIER) cc_final: 0.4762 (m-10)
REVERT: B  126 TYR cc_start: 0.5291 (OUTLIER) cc_final: 0.4807 (t80)
REVERT: B  165 TRP cc_start: 0.5099 (t-100) cc_final: 0.4323 (t-100)
REVERT: B  450 HIS cc_start: 0.6658 (OUTLIER) cc_final: 0.6252 (t-90)
  outliers start: 10
  outliers final: 6
  residues processed: 41
  average time/residue: 0.1035
  time to fit residues: 5.3157
Evaluate side-chains
  40 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   93 TRP
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  126 TYR
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  435 PHE
Chi-restraints excluded: chain B residue  450 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0980
   chunk 3 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0170
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.4818

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

Flipped N/Q/H residues before XYZ refinement:
** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.186241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.173287 restraints weight = 4993.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.176252 restraints weight = 2923.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.177960 restraints weight = 1957.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.4500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5640
moved from start:          0.4586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   2164  Z= 0.133
  Angle     :  0.716   7.188   2937  Z= 0.344
  Chirality :  0.040   0.118    340
  Planarity :  0.005   0.051    344
  Dihedral  :  5.106  36.194    275
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 23.71 %
    Favored  : 71.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.41 %

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:  1.26 (0.54), residues: 246
  helix:  1.58 (0.37), residues: 200
  sheet:  None (None), residues: 0
  loop : -2.58 (0.83), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 455 
 HIS   0.002   0.001   HIS B  59 
 PHE   0.024   0.002   PHE B 475 
 TYR   0.013   0.001   TYR B 468 
 ARG   0.001   0.000   ARG B  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03739 (  157)
  hydrogen bonds       : angle       4.16156 (  471)
  SS BOND              : bond        0.00270 (    2)
  SS BOND              : angle       3.18054 (    4)
  covalent geometry    : bond        0.00295 ( 2162)
  covalent geometry    : angle       0.70668 ( 2933)

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 33
  time to evaluate  : 0.242 
Fit side-chains
REVERT: B   93 TRP cc_start: 0.5282 (OUTLIER) cc_final: 0.4880 (m-10)
REVERT: B  126 TYR cc_start: 0.5258 (OUTLIER) cc_final: 0.4792 (t80)
REVERT: B  450 HIS cc_start: 0.6643 (OUTLIER) cc_final: 0.6293 (t-90)
  outliers start: 11
  outliers final: 8
  residues processed: 40
  average time/residue: 0.1025
  time to fit residues: 5.1678
Evaluate side-chains
  43 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   93 TRP
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  126 TYR
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  435 PHE
Chi-restraints excluded: chain B residue  436 MET
Chi-restraints excluded: chain B residue  438 ILE
Chi-restraints excluded: chain B residue  450 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0000
   chunk 8 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 7 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0770
   chunk 16 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.4942

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

Flipped N/Q/H residues before XYZ refinement:
** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.188231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.175073 restraints weight = 4937.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.177984 restraints weight = 2894.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.179981 restraints weight = 1960.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.4505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5642
moved from start:          0.4604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   2164  Z= 0.135
  Angle     :  0.732   7.178   2937  Z= 0.352
  Chirality :  0.040   0.132    340
  Planarity :  0.004   0.051    344
  Dihedral  :  5.173  35.106    275
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 23.71 %
    Favored  : 71.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.41 %

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:  1.05 (0.55), residues: 246
  helix:  1.46 (0.37), residues: 200
  sheet:  None (None), residues: 0
  loop : -2.78 (0.81), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 455 
 HIS   0.003   0.001   HIS B 167 
 PHE   0.024   0.002   PHE B 479 
 TYR   0.010   0.001   TYR B 468 
 ARG   0.001   0.000   ARG B  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03778 (  157)
  hydrogen bonds       : angle       4.13265 (  471)
  SS BOND              : bond        0.00266 (    2)
  SS BOND              : angle       3.07745 (    4)
  covalent geometry    : bond        0.00301 ( 2162)
  covalent geometry    : angle       0.72349 ( 2933)

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

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

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  492 Ramachandran restraints generated.
    246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
REVERT: B  126 TYR cc_start: 0.5233 (OUTLIER) cc_final: 0.4748 (t80)
REVERT: B  450 HIS cc_start: 0.6703 (OUTLIER) cc_final: 0.6321 (t-90)
  outliers start: 11
  outliers final: 8
  residues processed: 39
  average time/residue: 0.0930
  time to fit residues: 4.6811
Evaluate side-chains
  41 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 31
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   93 TRP
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  115 ILE
Chi-restraints excluded: chain B residue  126 TYR
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  435 PHE
Chi-restraints excluded: chain B residue  436 MET
Chi-restraints excluded: chain B residue  450 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 12 optimal weight:    0.2980
   chunk 8 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0470
   chunk 23 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 13 optimal weight:    0.3980
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.186264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.173173 restraints weight = 4948.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.176124 restraints weight = 2804.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.178202 restraints weight = 1854.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.4499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5620
moved from start:          0.4752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   2164  Z= 0.136
  Angle     :  0.734   7.409   2937  Z= 0.353
  Chirality :  0.041   0.152    340
  Planarity :  0.004   0.050    344
  Dihedral  :  5.162  34.853    275
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 22.84 %
    Favored  : 71.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.41 %

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:  1.17 (0.55), residues: 246
  helix:  1.57 (0.37), residues: 200
  sheet:  None (None), residues: 0
  loop : -2.87 (0.81), residues: 46

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 455 
 HIS   0.002   0.001   HIS B  59 
 PHE   0.024   0.002   PHE B 479 
 TYR   0.010   0.001   TYR B 468 
 ARG   0.001   0.000   ARG B  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03777 (  157)
  hydrogen bonds       : angle       4.12431 (  471)
  SS BOND              : bond        0.00282 (    2)
  SS BOND              : angle       3.02624 (    4)
  covalent geometry    : bond        0.00300 ( 2162)
  covalent geometry    : angle       0.72609 ( 2933)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1116.05 seconds
wall clock time: 20 minutes 14.37 seconds (1214.37 seconds total)