Starting phenix.real_space_refine
on Fri May  9 13:09:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9isi_60836/05_2025/9isi_60836_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9isi_60836/05_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_60836/05_2025/9isi_60836.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9isi_60836/05_2025/9isi_60836.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9isi_60836/05_2025/9isi_60836_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9isi_60836/05_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-5687/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: 2.64, per 1000 atoms: 1.35
  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: 0.54
  Conformation dependent library (CDL) restraints added in 296.1 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: 0.23
  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: 0.53

  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:             1.990
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     11.370
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.270
-------------------------------------------------------------------------------
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  : 0.220 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.2302
  time to fit residues: 8.2211
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  : 0.217 
-------------------------------------------------------------------------------
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 = 0.164639 restraints weight = 2357.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.167850 restraints weight = 1794.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.169798 restraints weight = 1532.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
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  : 0.219 
Fit side-chains
REVERT: B   50 LEU cc_start: 0.7399 (mp) cc_final: 0.7025 (tt)
  outliers start: 6
  outliers final: 4
  residues processed: 36
  average time/residue: 0.1906
  time to fit residues: 7.7927
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  : 0.221 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4403 r_free = 0.4403 target = 0.218395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.166453 restraints weight = 2387.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.167830 restraints weight = 2027.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.169714 restraints weight = 1848.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   2003  Z= 0.192
  Angle     :  0.630   7.441   2730  Z= 0.314
  Chirality :  0.042   0.166    343
  Planarity :  0.004   0.024    319
  Dihedral  :  3.611  12.462    260
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.21
  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:  1.65 (0.54), residues: 242
  helix:  1.66 (0.36), residues: 199
  sheet:  None (None), residues: 0
  loop : -1.58 (0.95), residues: 43

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 147 
 HIS   0.004   0.001   HIS B  63 
 PHE   0.017   0.002   PHE B 376 
 TYR   0.011   0.002   TYR B 356 
 ARG   0.002   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04795 (  149)
  hydrogen bonds       : angle       4.38207 (  444)
  covalent geometry    : bond        0.00461 ( 2003)
  covalent geometry    : angle       0.63038 ( 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
  44 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 33
  time to evaluate  : 0.224 
Fit side-chains
REVERT: B  153 MET cc_start: 0.6525 (mtp) cc_final: 0.6256 (mtp)
  outliers start: 11
  outliers final: 6
  residues processed: 40
  average time/residue: 0.1794
  time to fit residues: 8.1753
Evaluate side-chains
  38 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
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  449 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0980
   chunk 15 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0070
   chunk 4 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 3 optimal weight:    0.2980
   chunk 21 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 19 optimal weight:    0.3980
   overall best weight:    0.2998

-------------------------------------------------------------------------------
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 = 0.4441 r_free = 0.4441 target = 0.222581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.171869 restraints weight = 2404.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.173289 restraints weight = 2074.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.174529 restraints weight = 1897.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2003  Z= 0.123
  Angle     :  0.561   7.595   2730  Z= 0.275
  Chirality :  0.040   0.164    343
  Planarity :  0.004   0.023    319
  Dihedral  :  3.480  11.496    260
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 21.62 %
    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:  1.87 (0.55), residues: 242
  helix:  1.85 (0.37), residues: 199
  sheet:  None (None), residues: 0
  loop : -1.67 (0.93), residues: 43

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   0.014   0.001   PHE B 376 
 TYR   0.006   0.001   TYR B 160 
 ARG   0.001   0.000   ARG B 377 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03558 (  149)
  hydrogen bonds       : angle       4.04794 (  444)
  covalent geometry    : bond        0.00266 ( 2003)
  covalent geometry    : angle       0.56078 ( 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
  43 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 33
  time to evaluate  : 0.217 
Fit side-chains
REVERT: B   85 GLN cc_start: 0.4720 (tm-30) cc_final: 0.4335 (tm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 41
  average time/residue: 0.1687
  time to fit residues: 7.8811
Evaluate side-chains
  37 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Chi-restraints excluded: chain B residue  429 CYS
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:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0470
   overall best weight:    0.5478

-------------------------------------------------------------------------------
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 = 0.4405 r_free = 0.4405 target = 0.218661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.167503 restraints weight = 2468.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.169470 restraints weight = 2099.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.170093 restraints weight = 1904.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.2188

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= 0.159
  Angle     :  0.618   7.566   2730  Z= 0.300
  Chirality :  0.042   0.177    343
  Planarity :  0.004   0.024    319
  Dihedral  :  3.501  12.092    260
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 22.52 %
    Favored  : 72.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 : -1.79 (0.94), 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   0.002   PHE B 376 
 TYR   0.009   0.002   TYR B 356 
 ARG   0.001   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04240 (  149)
  hydrogen bonds       : angle       4.12974 (  444)
  covalent geometry    : bond        0.00376 ( 2003)
  covalent geometry    : angle       0.61825 ( 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
  43 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 33
  time to evaluate  : 0.207 
Fit side-chains
REVERT: B  153 MET cc_start: 0.6770 (mtp) cc_final: 0.6467 (mtp)
  outliers start: 10
  outliers final: 9
  residues processed: 39
  average time/residue: 0.1767
  time to fit residues: 7.8465
Evaluate side-chains
  40 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
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  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
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:    0.9990
   chunk 9 optimal weight:    0.2980
   chunk 16 optimal weight:    0.0870
   chunk 4 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0070
   chunk 22 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0030
   chunk 10 optimal weight:    0.0670
   chunk 1 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 24 optimal weight:    0.3980
   overall best weight:    0.0924

-------------------------------------------------------------------------------
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 = 0.4452 r_free = 0.4452 target = 0.222629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.173631 restraints weight = 2454.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.175440 restraints weight = 2061.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.176788 restraints weight = 1860.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   2003  Z= 0.113
  Angle     :  0.569   7.697   2730  Z= 0.274
  Chirality :  0.040   0.171    343
  Planarity :  0.004   0.025    319
  Dihedral  :  3.402  11.672    260
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 23.87 %
    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:  2.22 (0.55), residues: 242
  helix:  2.09 (0.37), residues: 200
  sheet:  None (None), residues: 0
  loop : -1.69 (0.95), 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 394 
 PHE   0.014   0.001   PHE B  34 
 TYR   0.005   0.001   TYR B 160 
 ARG   0.000   0.000   ARG B 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03244 (  149)
  hydrogen bonds       : angle       3.86584 (  444)
  covalent geometry    : bond        0.00222 ( 2003)
  covalent geometry    : angle       0.56931 ( 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
  40 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.213 
Fit side-chains
REVERT: B   85 GLN cc_start: 0.4806 (tm-30) cc_final: 0.4315 (tm-30)
REVERT: B  105 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7297 (p0)
REVERT: B  153 MET cc_start: 0.6795 (mtp) cc_final: 0.6403 (mtp)
  outliers start: 9
  outliers final: 6
  residues processed: 35
  average time/residue: 0.1778
  time to fit residues: 7.1260
Evaluate side-chains
  37 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 18 optimal weight:    0.0970
   chunk 22 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0050
   chunk 5 optimal weight:    0.0980
   chunk 3 optimal weight:    0.0970
   chunk 14 optimal weight:    0.6980
   chunk 0 optimal weight:    0.1980
   overall best weight:    0.0990

-------------------------------------------------------------------------------
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 = 0.4461 r_free = 0.4461 target = 0.224306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.175401 restraints weight = 2444.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.176856 restraints weight = 2043.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.178322 restraints weight = 1849.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   2003  Z= 0.110
  Angle     :  0.568   7.671   2730  Z= 0.270
  Chirality :  0.040   0.172    343
  Planarity :  0.004   0.022    319
  Dihedral  :  3.320  11.895    260
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 24.77 %
    Favored  : 71.62 %
  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:  2.40 (0.55), residues: 242
  helix:  2.18 (0.36), residues: 206
  sheet:  None (None), residues: 0
  loop : -2.08 (1.00), residues: 36

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   0.014   0.001   PHE B  34 
 TYR   0.005   0.001   TYR B 160 
 ARG   0.000   0.000   ARG B 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02978 (  149)
  hydrogen bonds       : angle       3.73083 (  444)
  covalent geometry    : bond        0.00220 ( 2003)
  covalent geometry    : angle       0.56799 ( 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  : 0.231 
Fit side-chains
REVERT: B   85 GLN cc_start: 0.4915 (tm-30) cc_final: 0.4417 (tm-30)
REVERT: B  105 ASN cc_start: 0.7636 (OUTLIER) cc_final: 0.7275 (p0)
REVERT: B  153 MET cc_start: 0.6698 (mtp) cc_final: 0.6410 (mtp)
  outliers start: 8
  outliers final: 7
  residues processed: 35
  average time/residue: 0.1789
  time to fit residues: 7.1636
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  : 0.221 
-------------------------------------------------------------------------------
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  105 ASN
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  380 VAL
Chi-restraints excluded: chain B residue  391 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0470
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    0.4980
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.6678

-------------------------------------------------------------------------------
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 = 0.4396 r_free = 0.4396 target = 0.217611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.166829 restraints weight = 2477.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.168626 restraints weight = 2039.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.170646 restraints weight = 1816.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   2003  Z= 0.177
  Angle     :  0.638   7.549   2730  Z= 0.307
  Chirality :  0.042   0.163    343
  Planarity :  0.004   0.025    319
  Dihedral  :  3.457  11.737    260
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 24.32 %
    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:  2.23 (0.55), residues: 242
  helix:  2.10 (0.37), residues: 200
  sheet:  None (None), residues: 0
  loop : -1.69 (0.95), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 416 
 HIS   0.004   0.001   HIS B  63 
 PHE   0.018   0.002   PHE B 376 
 TYR   0.011   0.002   TYR B 356 
 ARG   0.001   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04235 (  149)
  hydrogen bonds       : angle       4.03831 (  444)
  covalent geometry    : bond        0.00429 ( 2003)
  covalent geometry    : angle       0.63759 ( 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
  43 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 0.207 
Fit side-chains
REVERT: B  105 ASN cc_start: 0.7848 (OUTLIER) cc_final: 0.7445 (p0)
  outliers start: 11
  outliers final: 8
  residues processed: 39
  average time/residue: 0.1778
  time to fit residues: 7.8671
Evaluate side-chains
  41 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
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  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
Chi-restraints excluded: chain B residue  449 SER
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:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 6 optimal weight:    0.0970
   chunk 11 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 18 optimal weight:    0.2980
   chunk 17 optimal weight:    0.0570
   chunk 10 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.3296

-------------------------------------------------------------------------------
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 = 0.4422 r_free = 0.4422 target = 0.220129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.169281 restraints weight = 2577.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.171283 restraints weight = 2155.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.171283 restraints weight = 1933.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.2405

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= 0.127
  Angle     :  0.590   7.633   2730  Z= 0.282
  Chirality :  0.040   0.166    343
  Planarity :  0.004   0.024    319
  Dihedral  :  3.415  11.411    260
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 24.77 %
    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:  2.38 (0.55), residues: 242
  helix:  2.20 (0.36), residues: 200
  sheet:  None (None), residues: 0
  loop : -1.60 (0.97), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B 147 
 HIS   0.002   0.001   HIS B  63 
 PHE   0.015   0.001   PHE B  34 
 TYR   0.007   0.001   TYR B 356 
 ARG   0.001   0.000   ARG B 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03610 (  149)
  hydrogen bonds       : angle       3.89919 (  444)
  covalent geometry    : bond        0.00281 ( 2003)
  covalent geometry    : angle       0.59044 ( 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
  40 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 30
  time to evaluate  : 0.223 
Fit side-chains
REVERT: B  105 ASN cc_start: 0.7812 (OUTLIER) cc_final: 0.7392 (p0)
  outliers start: 10
  outliers final: 8
  residues processed: 35
  average time/residue: 0.1824
  time to fit residues: 7.2987
Evaluate side-chains
  39 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 30
  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  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  418 HIS
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:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 3 optimal weight:    0.4980
   chunk 23 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0980
   chunk 10 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.4404 r_free = 0.4404 target = 0.218425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.168036 restraints weight = 2434.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.169834 restraints weight = 2007.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.171694 restraints weight = 1794.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2003  Z= 0.155
  Angle     :  0.614   7.629   2730  Z= 0.296
  Chirality :  0.042   0.162    343
  Planarity :  0.004   0.024    319
  Dihedral  :  3.440  11.600    260
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 24.77 %
    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:  2.29 (0.55), residues: 242
  helix:  2.14 (0.36), residues: 200
  sheet:  None (None), residues: 0
  loop : -1.64 (0.97), 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  63 
 PHE   0.016   0.001   PHE B 376 
 TYR   0.009   0.001   TYR B 356 
 ARG   0.001   0.000   ARG B 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03952 (  149)
  hydrogen bonds       : angle       3.99275 (  444)
  covalent geometry    : bond        0.00368 ( 2003)
  covalent geometry    : angle       0.61359 ( 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
  41 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.217 
Fit side-chains
REVERT: B  105 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7387 (p0)
  outliers start: 9
  outliers final: 8
  residues processed: 37
  average time/residue: 0.1845
  time to fit residues: 7.7797
Evaluate side-chains
  40 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
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  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  418 HIS
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:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    0.2980
   chunk 2 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0770
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.5338

-------------------------------------------------------------------------------
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 = 0.4399 r_free = 0.4399 target = 0.217749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.167346 restraints weight = 2411.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.168916 restraints weight = 2050.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.170662 restraints weight = 1839.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2003  Z= 0.158
  Angle     :  0.619   7.620   2730  Z= 0.298
  Chirality :  0.042   0.162    343
  Planarity :  0.004   0.024    319
  Dihedral  :  3.476  11.793    260
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 24.32 %
    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:  2.34 (0.55), residues: 242
  helix:  2.17 (0.36), residues: 199
  sheet:  None (None), residues: 0
  loop : -1.53 (0.96), 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   0.009   0.001   TYR B 356 
 ARG   0.001   0.000   ARG B 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03992 (  149)
  hydrogen bonds       : angle       4.00794 (  444)
  covalent geometry    : bond        0.00373 ( 2003)
  covalent geometry    : angle       0.61890 ( 2730)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1211.53 seconds
wall clock time: 21 minutes 52.98 seconds (1312.98 seconds total)