Starting phenix.real_space_refine
on Sat Apr 26 15:25:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9isi_60836/04_2025/9isi_60836_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9isi_60836/04_2025/9isi_60836.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9isi_60836/04_2025/9isi_60836.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9isi_60836/04_2025/9isi_60836.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9isi_60836/04_2025/9isi_60836_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9isi_60836/04_2025/9isi_60836_neut.cif"
  }
  resolution = 3.56
  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=  -0.001 sd=   0.005
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      21      5.16       5
     C    1310      2.51       5
     N     311      2.21       5
     O     313      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 1955
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 1955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 252, 1955
          Classifications: {'peptide': 252}
          Link IDs: {'PTRANS': 12, 'TRANS': 239}
          Chain breaks: 4
  Time building chain proxies: 3.25, per 1000 atoms: 1.66
  Number of scatterers: 1955
  At special positions: 0
  Unit cell: (52.576, 72.928, 78.016, 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      21     16.00
     O     313      8.00
     N     311      7.00
     C    1310      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: 0.51
  Conformation dependent library (CDL) restraints added in 262.3 milliseconds
  

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  480

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 0 sheets defined
      91.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'B' and resid 22 through 36
    Processing helix  chain 'B' and resid 37 through 50
    Processing helix  chain 'B' and resid 57 through 73
      removed outlier: 3.913A  pdb=" N   PHE B  61 " --> pdb=" O   ASN B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 85
      removed outlier: 3.621A  pdb=" N   SER B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 97
    Processing helix  chain 'B' and resid 99 through 124
      removed outlier: 4.154A  pdb=" N   VAL B 103 " --> pdb=" O   PRO B  99 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   VAL B 124 " --> pdb=" O   ARG B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 130
      removed outlier: 3.581A  pdb=" N   TRP B 129 " --> pdb=" O   LYS B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 153
      removed outlier: 3.614A  pdb=" N   MET B 153 " --> pdb=" O   VAL B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 159
    Processing helix  chain 'B' and resid 332 through 345
      removed outlier: 3.758A  pdb=" N   THR B 337 " --> pdb=" O   LEU B 333 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   ILE B 338 " --> pdb=" O   VAL B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 365
      removed outlier: 3.536A  pdb=" N   SER B 349 " --> pdb=" O   PHE B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 403
      removed outlier: 3.706A  pdb=" N   ALA B 379 " --> pdb=" O   THR B 375 " (cutoff:3.500A)
      Proline residue:  B 392  - end of helix
    Processing helix  chain 'B' and resid 407 through 438
      removed outlier: 4.413A  pdb=" N   HIS B 418 " --> pdb=" O   MET B 414 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   VAL B 419 " --> pdb=" O   SER B 415 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   SER B 428 " --> pdb=" O   ALA B 424 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   CYS B 429 " --> pdb=" O   SER B 425 " (cutoff:3.500A)
      Proline residue:  B 432  - end of helix
      removed outlier: 4.058A  pdb=" N   TYR B 435 " --> pdb=" O   ASN B 431 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   ALA B 436 " --> pdb=" O   PRO B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 459
      removed outlier: 3.903A  pdb=" N   ALA B 456 " --> pdb=" O   GLY B 452 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   ALA B 457 " --> pdb=" O   ILE B 453 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   PHE B 458 " --> pdb=" O   LEU B 454 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   SER B 459 " --> pdb=" O   GLU B 455 " (cutoff:3.500A)

    149 hydrogen bonds defined for protein.
    444 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: 0.55

  Time building geometry restraints manager: 0.62 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: 451
        1.34 -     1.45: 381
        1.45 -     1.57: 1142
        1.57 -     1.69: 0
        1.69 -     1.81: 29
  Bond restraints: 2003
  Sorted by residual:
  bond pdb=" C   THR B 339 "
       pdb=" N   ARG B 340 "
    ideal  model  delta    sigma   weight residual
    1.334  1.290  0.045 1.27e-02 6.20e+03 1.25e+01
  bond pdb=" C   ARG B 340 "
       pdb=" N   LEU B 341 "
    ideal  model  delta    sigma   weight residual
    1.335  1.379 -0.044 1.31e-02 5.83e+03 1.15e+01
  bond pdb=" N   LEU B  50 "
       pdb=" CA  LEU B  50 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.037 1.16e-02 7.43e+03 1.03e+01
  bond pdb=" N   LEU B  97 "
       pdb=" CA  LEU B  97 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.30e-02 5.92e+03 7.00e+00
  bond pdb=" N   LEU B 413 "
       pdb=" CA  LEU B 413 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.23e-02 6.61e+03 6.00e+00
  ... (remaining 1998 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.06: 2514
        1.06 -     2.11: 150
        2.11 -     3.17: 48
        3.17 -     4.22: 13
        4.22 -     5.28: 5
  Bond angle restraints: 2730
  Sorted by residual:
  angle pdb=" O   ARG B 340 "
        pdb=" C   ARG B 340 "
        pdb=" N   LEU B 341 "
      ideal   model   delta    sigma   weight residual
     122.07  125.50   -3.43 1.03e+00 9.43e-01 1.11e+01
  angle pdb=" CA  LEU B 413 "
        pdb=" C   LEU B 413 "
        pdb=" O   LEU B 413 "
      ideal   model   delta    sigma   weight residual
     120.42  117.20    3.22 1.06e+00 8.90e-01 9.23e+00
  angle pdb=" N   PRO B  99 "
        pdb=" CA  PRO B  99 "
        pdb=" C   PRO B  99 "
      ideal   model   delta    sigma   weight residual
     114.18  109.96    4.22 1.39e+00 5.18e-01 9.22e+00
  angle pdb=" C   PRO B 432 "
        pdb=" CA  PRO B 432 "
        pdb=" CB  PRO B 432 "
      ideal   model   delta    sigma   weight residual
     111.85  108.07    3.78 1.42e+00 4.96e-01 7.08e+00
  angle pdb=" N   MET B 138 "
        pdb=" CA  MET B 138 "
        pdb=" C   MET B 138 "
      ideal   model   delta    sigma   weight residual
     111.28  108.44    2.84 1.09e+00 8.42e-01 6.80e+00
  ... (remaining 2725 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.83: 952
       10.83 -    21.66: 121
       21.66 -    32.50: 64
       32.50 -    43.33: 25
       43.33 -    54.16: 6
  Dihedral angle restraints: 1168
    sinusoidal: 436
      harmonic: 732
  Sorted by residual:
  dihedral pdb=" N   MET B 363 "
           pdb=" CA  MET B 363 "
           pdb=" CB  MET B 363 "
           pdb=" CG  MET B 363 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -129.25  -50.75     3      1.50e+01 4.44e-03 8.94e+00
  dihedral pdb=" CA  LEU B  70 "
           pdb=" CB  LEU B  70 "
           pdb=" CG  LEU B  70 "
           pdb=" CD1 LEU B  70 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  130.32   49.68     3      1.50e+01 4.44e-03 8.81e+00
  dihedral pdb=" CA  GLN B  85 "
           pdb=" CB  GLN B  85 "
           pdb=" CG  GLN B  85 "
           pdb=" CD  GLN B  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -105.90   45.90     3      1.50e+01 4.44e-03 8.25e+00
  ... (remaining 1165 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 230
       0.036 -    0.072: 85
       0.072 -    0.107: 19
       0.107 -    0.143: 6
       0.143 -    0.179: 3
  Chirality restraints: 343
  Sorted by residual:
  chirality pdb=" CA  THR B 391 "
            pdb=" N   THR B 391 "
            pdb=" C   THR B 391 "
            pdb=" CB  THR B 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.18 2.00e-01 2.50e+01 8.01e-01
  chirality pdb=" CA  MET B 138 "
            pdb=" N   MET B 138 "
            pdb=" C   MET B 138 "
            pdb=" CB  MET B 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.70e-01
  chirality pdb=" CA  MET B 106 "
            pdb=" N   MET B 106 "
            pdb=" C   MET B 106 "
            pdb=" CB  MET B 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.26e-01
  ... (remaining 340 not shown)

  Planarity restraints: 319
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  98 "    0.006 2.00e-02 2.50e+03   1.10e-02 1.20e+00
        pdb=" C   ILE B  98 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   ILE B  98 "    0.007 2.00e-02 2.50e+03
        pdb=" N   PRO B  99 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 404 "    0.015 5.00e-02 4.00e+02   2.33e-02 8.70e-01
        pdb=" N   PRO B 405 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO B 405 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO B 405 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  34 "    0.008 2.00e-02 2.50e+03   6.97e-03 8.50e-01
        pdb=" CG  PHE B  34 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  34 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  34 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  34 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  34 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  34 "    0.000 2.00e-02 2.50e+03
  ... (remaining 316 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 772
        2.90 -     3.40: 2096
        3.40 -     3.90: 3105
        3.90 -     4.40: 3132
        4.40 -     4.90: 5488
  Nonbonded interactions: 14593
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 105 "
            pdb=" N   MET B 106 "
     model   vdw
     2.397 3.120
  nonbonded pdb=" O   LYS B 411 "
            pdb=" OG  SER B 415 "
     model   vdw
     2.414 3.040
  nonbonded pdb=" O   LEU B 409 "
            pdb=" OG1 THR B 412 "
     model   vdw
     2.448 3.040
  nonbonded pdb=" O   VAL B  23 "
            pdb=" OG  SER B  26 "
     model   vdw
     2.470 3.040
  nonbonded pdb=" O   ILE B 102 "
            pdb=" OD1 ASN B 105 "
     model   vdw
     2.508 3.040
  ... (remaining 14588 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.450
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     12.630
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6569
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   0.045   2003  Z= 0.292
  Angle     :  0.666   5.277   2730  Z= 0.421
  Chirality :  0.043   0.179    343
  Planarity :  0.003   0.023    319
  Dihedral  : 14.084  54.158    688
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 21.62 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.57), residues: 242
  helix:  1.70 (0.38), residues: 198
  sheet:  None (None), residues: 0
  loop : -2.37 (0.94), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 147 
 HIS   0.002   0.001   HIS B  63 
 PHE   0.016   0.001   PHE B  34 
 TYR   0.007   0.001   TYR B 393 
 ARG   0.001   0.000   ARG B 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10151 (  149)
  hydrogen bonds       : angle       5.33603 (  444)
  covalent geometry    : bond        0.00457 ( 2003)
  covalent geometry    : angle       0.66597 ( 2730)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.216 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.2264
  time to fit residues: 8.1024
Evaluate side-chains
  31 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 18 optimal weight:    0.0980
   chunk 10 optimal weight:    0.2980
   chunk 6 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.4380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.217709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.164641 restraints weight = 2357.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.167762 restraints weight = 1794.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.169886 restraints weight = 1533.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.1085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2003  Z= 0.147
  Angle     :  0.584   6.987   2730  Z= 0.288
  Chirality :  0.041   0.166    343
  Planarity :  0.004   0.027    319
  Dihedral  :  3.466  11.499    260
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 20.27 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.55), residues: 242
  helix:  1.94 (0.36), residues: 198
  sheet:  None (None), residues: 0
  loop : -1.11 (1.00), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 147 
 HIS   0.003   0.001   HIS B  63 
 PHE   0.014   0.001   PHE B  34 
 TYR   0.008   0.001   TYR B 160 
 ARG   0.003   0.000   ARG B 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04192 (  149)
  hydrogen bonds       : angle       4.33863 (  444)
  covalent geometry    : bond        0.00329 ( 2003)
  covalent geometry    : angle       0.58413 ( 2730)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.237 
Fit side-chains
REVERT: B   50 LEU cc_start: 0.7395 (mp) cc_final: 0.7021 (tt)
  outliers start: 6
  outliers final: 4
  residues processed: 36
  average time/residue: 0.1932
  time to fit residues: 7.9275
Evaluate side-chains
  36 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  449 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 2 optimal weight:    0.0470
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    0.4980
   chunk 0 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.5078

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.220537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.169024 restraints weight = 2410.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.170362 restraints weight = 2065.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.171438 restraints weight = 1893.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   2003  Z= 0.154
  Angle     :  0.594   7.388   2730  Z= 0.293
  Chirality :  0.041   0.168    343
  Planarity :  0.004   0.024    319
  Dihedral  :  3.531  11.968    260
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 19.37 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.54), residues: 242
  helix:  1.77 (0.36), residues: 199
  sheet:  None (None), residues: 0
  loop : -1.55 (0.96), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 147 
 HIS   0.003   0.001   HIS B  63 
 PHE   0.015   0.001   PHE B  34 
 TYR   0.009   0.002   TYR B 356 
 ARG   0.001   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04196 (  149)
  hydrogen bonds       : angle       4.19461 (  444)
  covalent geometry    : bond        0.00359 ( 2003)
  covalent geometry    : angle       0.59358 ( 2730)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 35
  time to evaluate  : 0.239 
Fit side-chains
REVERT: B   85 GLN cc_start: 0.4796 (tm-30) cc_final: 0.4421 (tm-30)
  outliers start: 11
  outliers final: 5
  residues processed: 42
  average time/residue: 0.1784
  time to fit residues: 8.5806
Evaluate side-chains
  38 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  449 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0170
   chunk 4 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 19 optimal weight:    0.4980
   overall best weight:    0.5018

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.219866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.168821 restraints weight = 2395.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.170496 restraints weight = 2070.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.171277 restraints weight = 1892.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   2003  Z= 0.150
  Angle     :  0.588   7.602   2730  Z= 0.289
  Chirality :  0.041   0.175    343
  Planarity :  0.004   0.023    319
  Dihedral  :  3.524  12.002    260
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 21.17 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.55), residues: 242
  helix:  1.80 (0.37), residues: 200
  sheet:  None (None), residues: 0
  loop : -1.72 (0.95), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 147 
 HIS   0.003   0.001   HIS B 133 
 PHE   0.015   0.001   PHE B 376 
 TYR   0.008   0.001   TYR B 356 
 ARG   0.001   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04031 (  149)
  hydrogen bonds       : angle       4.13935 (  444)
  covalent geometry    : bond        0.00352 ( 2003)
  covalent geometry    : angle       0.58819 ( 2730)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 33
  time to evaluate  : 0.220 
Fit side-chains
REVERT: B   85 GLN cc_start: 0.4784 (tm-30) cc_final: 0.4383 (tm-30)
REVERT: B  153 MET cc_start: 0.6779 (mtp) cc_final: 0.6465 (mtp)
  outliers start: 11
  outliers final: 7
  residues processed: 41
  average time/residue: 0.1798
  time to fit residues: 8.3966
Evaluate side-chains
  38 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  449 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 2 optimal weight:    0.4980
   chunk 18 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0970
   overall best weight:    0.4978

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.219495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.168380 restraints weight = 2470.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.170233 restraints weight = 2097.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.171003 restraints weight = 1908.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2003  Z= 0.151
  Angle     :  0.612   7.693   2730  Z= 0.296
  Chirality :  0.041   0.168    343
  Planarity :  0.004   0.024    319
  Dihedral  :  3.510  11.825    260
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 22.07 %
    Favored  : 72.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.55), residues: 242
  helix:  1.84 (0.37), residues: 199
  sheet:  None (None), residues: 0
  loop : -1.66 (0.92), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 147 
 HIS   0.003   0.001   HIS B  63 
 PHE   0.016   0.001   PHE B 376 
 TYR   0.008   0.001   TYR B 356 
 ARG   0.001   0.000   ARG B 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04064 (  149)
  hydrogen bonds       : angle       4.13245 (  444)
  covalent geometry    : bond        0.00355 ( 2003)
  covalent geometry    : angle       0.61224 ( 2730)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 32
  time to evaluate  : 0.221 
Fit side-chains
  outliers start: 13
  outliers final: 10
  residues processed: 41
  average time/residue: 0.1746
  time to fit residues: 8.1902
Evaluate side-chains
  41 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 31
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  429 CYS
Chi-restraints excluded: chain B residue  449 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 16 optimal weight:    0.4980
   chunk 4 optimal weight:    0.5980
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 10 optimal weight:    0.4980
   chunk 1 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 394 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.217720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.166656 restraints weight = 2469.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.167936 restraints weight = 2125.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.169510 restraints weight = 1948.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2003  Z= 0.168
  Angle     :  0.633   7.627   2730  Z= 0.308
  Chirality :  0.042   0.165    343
  Planarity :  0.004   0.025    319
  Dihedral  :  3.571  12.492    260
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 22.52 %
    Favored  : 72.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.55), residues: 242
  helix:  1.75 (0.37), residues: 199
  sheet:  None (None), residues: 0
  loop : -1.66 (0.93), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 147 
 HIS   0.003   0.001   HIS B  63 
 PHE   0.017   0.002   PHE B 376 
 TYR   0.009   0.002   TYR B 356 
 ARG   0.001   0.000   ARG B 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04354 (  149)
  hydrogen bonds       : angle       4.18373 (  444)
  covalent geometry    : bond        0.00402 ( 2003)
  covalent geometry    : angle       0.63263 ( 2730)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 29
  time to evaluate  : 0.238 
Fit side-chains
  outliers start: 12
  outliers final: 8
  residues processed: 38
  average time/residue: 0.1870
  time to fit residues: 8.1772
Evaluate side-chains
  37 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 29
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  337 THR
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  429 CYS
Chi-restraints excluded: chain B residue  449 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 18 optimal weight:    0.3980
   chunk 22 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 12 optimal weight:    0.1980
   chunk 1 optimal weight:    0.0040
   chunk 2 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0770
   chunk 0 optimal weight:    0.2980
   overall best weight:    0.1950

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

Flipped N/Q/H residues before XYZ refinement:
B 105 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.222544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.173837 restraints weight = 2430.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.175436 restraints weight = 2082.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.176870 restraints weight = 1878.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   2003  Z= 0.113
  Angle     :  0.577   7.706   2730  Z= 0.277
  Chirality :  0.040   0.161    343
  Planarity :  0.004   0.026    319
  Dihedral  :  3.411  11.541    260
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 25.23 %
    Favored  : 71.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.55), residues: 242
  helix:  2.01 (0.37), residues: 200
  sheet:  None (None), residues: 0
  loop : -1.82 (0.92), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B 147 
 HIS   0.001   0.000   HIS B 133 
 PHE   0.014   0.001   PHE B  34 
 TYR   0.005   0.001   TYR B 160 
 ARG   0.001   0.000   ARG B 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03197 (  149)
  hydrogen bonds       : angle       3.82978 (  444)
  covalent geometry    : bond        0.00236 ( 2003)
  covalent geometry    : angle       0.57689 ( 2730)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 30
  time to evaluate  : 0.199 
Fit side-chains
REVERT: B  105 ASN cc_start: 0.7707 (OUTLIER) cc_final: 0.7316 (p0)
  outliers start: 8
  outliers final: 5
  residues processed: 37
  average time/residue: 0.1687
  time to fit residues: 7.1796
Evaluate side-chains
  34 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  105 ASN
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  429 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0170
   chunk 19 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   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 105 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.224194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 93)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.203590 restraints weight = 2345.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.203590 restraints weight = 3455.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.203590 restraints weight = 3455.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.4055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2003  Z= 0.148
  Angle     :  0.607   7.696   2730  Z= 0.292
  Chirality :  0.041   0.162    343
  Planarity :  0.004   0.025    319
  Dihedral  :  3.418  11.476    260
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 25.68 %
    Favored  : 70.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.55), residues: 242
  helix:  2.04 (0.37), residues: 200
  sheet:  None (None), residues: 0
  loop : -1.87 (0.93), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 147 
 HIS   0.003   0.001   HIS B  63 
 PHE   0.016   0.001   PHE B 376 
 TYR   0.009   0.001   TYR B 356 
 ARG   0.004   0.000   ARG B 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03819 (  149)
  hydrogen bonds       : angle       3.93320 (  444)
  covalent geometry    : bond        0.00345 ( 2003)
  covalent geometry    : angle       0.60675 ( 2730)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 29
  time to evaluate  : 0.222 
Fit side-chains
REVERT: B  105 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.7267 (p0)
  outliers start: 8
  outliers final: 6
  residues processed: 34
  average time/residue: 0.1832
  time to fit residues: 7.1576
Evaluate side-chains
  36 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 29
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  105 ASN
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  418 HIS
Chi-restraints excluded: chain B residue  429 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0970
   chunk 6 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 14 optimal weight:    0.1980
   chunk 7 optimal weight:    0.1980
   chunk 18 optimal weight:    0.0770
   chunk 17 optimal weight:    0.6980
   chunk 10 optimal weight:    8.9990
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.2336

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

Flipped N/Q/H residues before XYZ refinement:
B 105 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.226081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 104)---------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.195464 restraints weight = 2384.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.195281 restraints weight = 2379.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.195266 restraints weight = 2351.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2003  Z= 0.119
  Angle     :  0.589   7.751   2730  Z= 0.282
  Chirality :  0.040   0.160    343
  Planarity :  0.004   0.025    319
  Dihedral  :  3.378  11.377    260
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 25.68 %
    Favored  : 70.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.32 (0.55), residues: 242
  helix:  2.18 (0.37), residues: 200
  sheet:  None (None), residues: 0
  loop : -1.78 (0.94), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B 147 
 HIS   0.001   0.000   HIS B  63 
 PHE   0.015   0.001   PHE B  34 
 TYR   0.006   0.001   TYR B 356 
 ARG   0.004   0.000   ARG B 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03340 (  149)
  hydrogen bonds       : angle       3.81447 (  444)
  covalent geometry    : bond        0.00252 ( 2003)
  covalent geometry    : angle       0.58943 ( 2730)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.224 
Fit side-chains
REVERT: B  105 ASN cc_start: 0.7604 (OUTLIER) cc_final: 0.7303 (p0)
REVERT: B  365 ARG cc_start: 0.6161 (tmm-80) cc_final: 0.5763 (tpp-160)
  outliers start: 8
  outliers final: 5
  residues processed: 34
  average time/residue: 0.1796
  time to fit residues: 7.0096
Evaluate side-chains
  34 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  105 ASN
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  429 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0970
   chunk 18 optimal weight:    0.0770
   chunk 10 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.4736

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

Flipped N/Q/H residues before XYZ refinement:
B 105 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.224470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.202798 restraints weight = 2295.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 75)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.188222 restraints weight = 3650.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.189053 restraints weight = 3198.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2003  Z= 0.149
  Angle     :  0.616   7.719   2730  Z= 0.296
  Chirality :  0.041   0.161    343
  Planarity :  0.004   0.024    319
  Dihedral  :  3.414  11.299    260
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 25.68 %
    Favored  : 70.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.55), residues: 242
  helix:  2.11 (0.36), residues: 200
  sheet:  None (None), residues: 0
  loop : -1.89 (0.93), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 147 
 HIS   0.002   0.001   HIS B  63 
 PHE   0.016   0.001   PHE B 376 
 TYR   0.008   0.001   TYR B 356 
 ARG   0.003   0.000   ARG B 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03759 (  149)
  hydrogen bonds       : angle       3.91508 (  444)
  covalent geometry    : bond        0.00349 ( 2003)
  covalent geometry    : angle       0.61556 ( 2730)

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

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

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  484 Ramachandran restraints generated.
    242 Oldfield, 0 Emsley, 242 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.229 
Fit side-chains
REVERT: B  105 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.7346 (p0)
REVERT: B  365 ARG cc_start: 0.6038 (tmm-80) cc_final: 0.5715 (tpp-160)
  outliers start: 8
  outliers final: 6
  residues processed: 35
  average time/residue: 0.1986
  time to fit residues: 8.0006
Evaluate side-chains
  35 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  105 ASN
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  429 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 6 optimal weight:    0.2980
   chunk 12 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 23 optimal weight:    0.2980
   chunk 15 optimal weight:    0.2980
   chunk 19 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
B 105 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.224904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.205516 restraints weight = 2268.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.205516 restraints weight = 3394.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.205516 restraints weight = 3394.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2003  Z= 0.133
  Angle     :  0.600   7.777   2730  Z= 0.289
  Chirality :  0.041   0.162    343
  Planarity :  0.004   0.026    319
  Dihedral  :  3.398  11.212    260
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 26.58 %
    Favored  : 70.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.55), residues: 242
  helix:  2.16 (0.36), residues: 200
  sheet:  None (None), residues: 0
  loop : -1.88 (0.94), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP B 147 
 HIS   0.002   0.001   HIS B  63 
 PHE   0.015   0.001   PHE B 376 
 TYR   0.007   0.001   TYR B 356 
 ARG   0.004   0.000   ARG B 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03615 (  149)
  hydrogen bonds       : angle       3.88643 (  444)
  covalent geometry    : bond        0.00301 ( 2003)
  covalent geometry    : angle       0.60048 ( 2730)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1319.26 seconds
wall clock time: 23 minutes 36.70 seconds (1416.70 seconds total)