Starting phenix.real_space_refine
on Wed Jul 23 12:29:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yd1_33745/07_2025/7yd1_33745.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yd1_33745/07_2025/7yd1_33745.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yd1_33745/07_2025/7yd1_33745.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yd1_33745/07_2025/7yd1_33745.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yd1_33745/07_2025/7yd1_33745.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yd1_33745/07_2025/7yd1_33745.cif"
  }
  resolution = 2.99
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
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      16      5.16       5
     C    2104      2.51       5
     N     550      2.21       5
     O     635      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3305
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1588
          Classifications: {'peptide': 198}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 185}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 931
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 7, 'TRANS': 114}
    Chain: "B"
      Number of atoms: 786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 786
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
  Time building chain proxies: 2.74, per 1000 atoms: 0.83
  Number of scatterers: 3305
  At special positions: 0
  Unit cell: (84.056, 84.056, 92.568, 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      16     16.00
     O     635      8.00
     N     550      7.00
     C    2104      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  90 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 398.3 milliseconds
  

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  792

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 9 sheets defined
      6.8% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 364 through 370
    Processing helix  chain 'C' and resid 406 through 410
    Processing helix  chain 'C' and resid 417 through 422
    Processing helix  chain 'B' and resid 81 through 85
      removed outlier: 3.523A  pdb=" N   ASP B  84 " --> pdb=" O   GLN B  81 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   GLU B  85 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 81 through 85'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.532A  pdb=" N   ALA C 397 " --> pdb=" O   LYS C 356 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   VAL C 433 " --> pdb=" O   LYS C 378 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.542A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 473 through 474
      removed outlier: 3.508A  pdb=" N   TYR C 473 " --> pdb=" O   TYR C 489 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   TYR C 489 " --> pdb=" O   TYR C 473 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 3 through 6
    Processing sheet with id=AA5, first strand: chain 'A' and resid 11 through 12
    Processing sheet with id=AA6, first strand: chain 'A' and resid 37 through 40
      removed outlier: 6.657A  pdb=" N   TRP A  38 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 12
    Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 23
    Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 50
      removed outlier: 6.771A  pdb=" N   TRP B  37 " --> pdb=" O   MET B  49 " (cutoff:3.500A)

    77 hydrogen bonds defined for protein.
    177 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: 0.74

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1045
        1.34 -     1.46: 849
        1.46 -     1.58: 1476
        1.58 -     1.69: 0
        1.69 -     1.81: 19
  Bond restraints: 3389
  Sorted by residual:
  bond pdb=" N   ASP B  52 "
       pdb=" CA  ASP B  52 "
    ideal  model  delta    sigma   weight residual
    1.457  1.467 -0.010 1.32e-02 5.74e+03 5.68e-01
  bond pdb=" C   SER A  67 "
       pdb=" N   SER A  68 "
    ideal  model  delta    sigma   weight residual
    1.332  1.323  0.009 1.40e-02 5.10e+03 4.49e-01
  bond pdb=" CA  PHE A 107 "
       pdb=" C   PHE A 107 "
    ideal  model  delta    sigma   weight residual
    1.531  1.524  0.007 1.08e-02 8.57e+03 4.23e-01
  bond pdb=" CG  PRO A  89 "
       pdb=" CD  PRO A  89 "
    ideal  model  delta    sigma   weight residual
    1.503  1.486  0.017 3.40e-02 8.65e+02 2.47e-01
  bond pdb=" C   TYR B  51 "
       pdb=" N   ASP B  52 "
    ideal  model  delta    sigma   weight residual
    1.332  1.339 -0.006 1.37e-02 5.33e+03 2.17e-01
  ... (remaining 3384 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 4552
        1.82 -     3.63: 63
        3.63 -     5.45: 3
        5.45 -     7.26: 0
        7.26 -     9.08: 1
  Bond angle restraints: 4619
  Sorted by residual:
  angle pdb=" N   VAL B  53 "
        pdb=" CA  VAL B  53 "
        pdb=" C   VAL B  53 "
      ideal   model   delta    sigma   weight residual
     109.34  113.82   -4.48 2.08e+00 2.31e-01 4.63e+00
  angle pdb=" CA  TYR B  51 "
        pdb=" CB  TYR B  51 "
        pdb=" CG  TYR B  51 "
      ideal   model   delta    sigma   weight residual
     113.90  117.74   -3.84 1.80e+00 3.09e-01 4.56e+00
  angle pdb=" C   ASP B  52 "
        pdb=" N   VAL B  53 "
        pdb=" CA  VAL B  53 "
      ideal   model   delta    sigma   weight residual
     121.97  125.50   -3.53 1.80e+00 3.09e-01 3.85e+00
  angle pdb=" CA  PHE A 107 "
        pdb=" C   PHE A 107 "
        pdb=" N   ASP A 108 "
      ideal   model   delta    sigma   weight residual
     114.17  117.17   -3.00 1.55e+00 4.16e-01 3.75e+00
  angle pdb=" C   TYR B  51 "
        pdb=" N   ASP B  52 "
        pdb=" CA  ASP B  52 "
      ideal   model   delta    sigma   weight residual
     121.31  124.15   -2.84 1.49e+00 4.50e-01 3.63e+00
  ... (remaining 4614 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.48: 1791
        9.48 -    18.96: 128
       18.96 -    28.44: 62
       28.44 -    37.93: 24
       37.93 -    47.41: 4
  Dihedral angle restraints: 2009
    sinusoidal: 766
      harmonic: 1243
  Sorted by residual:
  dihedral pdb=" CA  ASP B  52 "
           pdb=" C   ASP B  52 "
           pdb=" N   VAL B  53 "
           pdb=" CA  VAL B  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.24  -23.76     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" CA  TYR B  51 "
           pdb=" C   TYR B  51 "
           pdb=" N   ASP B  52 "
           pdb=" CA  ASP B  52 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.50  -18.50     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  SER B  26 "
           pdb=" C   SER B  26 "
           pdb=" N   SER B  27 "
           pdb=" CA  SER B  27 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.42  -17.58     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 2006 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 279
       0.024 -    0.048: 143
       0.048 -    0.072: 48
       0.072 -    0.096: 26
       0.096 -    0.120: 20
  Chirality restraints: 516
  Sorted by residual:
  chirality pdb=" CA  ILE B  20 "
            pdb=" N   ILE B  20 "
            pdb=" C   ILE B  20 "
            pdb=" CB  ILE B  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.59e-01
  chirality pdb=" CA  VAL B  98 "
            pdb=" N   VAL B  98 "
            pdb=" C   VAL B  98 "
            pdb=" CB  VAL B  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.59e-01
  chirality pdb=" CA  ILE B  77 "
            pdb=" N   ILE B  77 "
            pdb=" C   ILE B  77 "
            pdb=" CB  ILE B  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.49e-01
  ... (remaining 513 not shown)

  Planarity restraints: 590
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 462 "    0.034 5.00e-02 4.00e+02   5.16e-02 4.26e+00
        pdb=" N   PRO C 463 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO C 463 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO C 463 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  88 "   -0.023 5.00e-02 4.00e+02   3.47e-02 1.92e+00
        pdb=" N   PRO A  89 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A  89 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A  89 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 383 "    0.019 5.00e-02 4.00e+02   2.88e-02 1.33e+00
        pdb=" N   PRO C 384 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO C 384 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 384 "    0.016 5.00e-02 4.00e+02
  ... (remaining 587 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 319
        2.75 -     3.29: 3186
        3.29 -     3.83: 5375
        3.83 -     4.36: 6403
        4.36 -     4.90: 11033
  Nonbonded interactions: 26316
  Sorted by model distance:
  nonbonded pdb=" OG  SER A   7 "
            pdb=" OG1 THR A  21 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OG1 THR B   5 "
            pdb=" OG1 THR B  23 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OG1 THR A  70 "
            pdb=" OG1 THR A  83 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   ILE A 106 "
            pdb=" OH  TYR B  38 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   THR C 393 "
            pdb=" OG1 THR C 523 "
     model   vdw
     2.310 3.040
  ... (remaining 26311 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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 individual isotropic
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:             1.530
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.520
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
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      :  0.002   0.017   3395  Z= 0.085
  Angle     :  0.491   9.075   4631  Z= 0.261
  Chirality :  0.039   0.120    516
  Planarity :  0.004   0.052    590
  Dihedral  :  8.999  47.407   1199
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.95 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  :  5.19 %
    Favored  : 89.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.06 (0.37), residues: 422
  helix: -5.17 (0.22), residues: 20
  sheet: -1.77 (0.41), residues: 144
  loop : -3.20 (0.35), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 436 
 HIS   0.000   0.000   HIS B  41 
 PHE   0.007   0.001   PHE C 429 
 TYR   0.018   0.001   TYR B  51 
 ARG   0.002   0.000   ARG C 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18925 (   77)
  hydrogen bonds       : angle       9.28182 (  177)
  SS BOND              : bond        0.00101 (    6)
  SS BOND              : angle       0.31712 (   12)
  covalent geometry    : bond        0.00165 ( 3389)
  covalent geometry    : angle       0.49117 ( 4619)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.281 
Fit side-chains
REVERT: C  346 ARG cc_start: 0.6893 (tpt90) cc_final: 0.6617 (tpt90)
REVERT: C  392 PHE cc_start: 0.8236 (m-80) cc_final: 0.8025 (m-80)
REVERT: C  395 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8421 (m)
REVERT: C  399 SER cc_start: 0.8317 (m) cc_final: 0.7941 (p)
REVERT: C  429 PHE cc_start: 0.7342 (t80) cc_final: 0.7096 (t80)
REVERT: C  437 ASN cc_start: 0.7918 (t0) cc_final: 0.7672 (t0)
REVERT: C  438 SER cc_start: 0.8450 (p) cc_final: 0.8188 (p)
REVERT: C  455 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7534 (tm)
REVERT: C  456 PHE cc_start: 0.6700 (m-80) cc_final: 0.6210 (m-80)
REVERT: C  494 SER cc_start: 0.8374 (t) cc_final: 0.8150 (p)
REVERT: C  515 PHE cc_start: 0.8611 (m-10) cc_final: 0.8263 (m-10)
REVERT: A   18 LEU cc_start: 0.8044 (mt) cc_final: 0.7368 (mp)
REVERT: A   47 LEU cc_start: 0.8403 (mt) cc_final: 0.8120 (mt)
REVERT: A   52 LEU cc_start: 0.8743 (tp) cc_final: 0.8466 (tp)
REVERT: A   61 TYR cc_start: 0.8444 (m-80) cc_final: 0.7757 (m-80)
REVERT: A   87 MET cc_start: 0.6147 (mmm) cc_final: 0.5527 (mmm)
REVERT: A  107 PHE cc_start: 0.8136 (m-10) cc_final: 0.7886 (m-10)
REVERT: A  112 GLN cc_start: 0.6423 (pp30) cc_final: 0.6127 (pp30)
  outliers start: 20
  outliers final: 5
  residues processed: 124
  average time/residue: 0.6032
  time to fit residues: 79.1868
Evaluate side-chains
  107 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  455 LEU
Chi-restraints excluded: chain A residue   92 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 16 optimal weight:    0.4980
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0980
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0770
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
C 388 ASN
C 409 GLN
C 460 ASN
C 506 GLN
A  16 GLN
A  78 ASN
A  79 GLN
B  39 GLN
B  41 HIS
B  81 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.133218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.121508 restraints weight = 5068.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 2.37
r_work: 0.3509 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3351 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
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      :  0.005   0.060   3395  Z= 0.231
  Angle     :  0.646  11.567   4631  Z= 0.323
  Chirality :  0.045   0.211    516
  Planarity :  0.005   0.058    590
  Dihedral  :  5.801  45.312    479
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.61 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 12.57 %
    Favored  : 82.51 %
  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: -3.37 (0.38), residues: 422
  helix: -5.23 (0.23), residues: 12
  sheet: -1.45 (0.41), residues: 146
  loop : -2.69 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  49 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.011   0.001   PHE A  24 
 TYR   0.016   0.002   TYR B  51 
 ARG   0.003   0.000   ARG C 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03764 (   77)
  hydrogen bonds       : angle       6.73334 (  177)
  SS BOND              : bond        0.00328 (    6)
  SS BOND              : angle       0.75357 (   12)
  covalent geometry    : bond        0.00513 ( 3389)
  covalent geometry    : angle       0.64529 ( 4619)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.335 
Fit side-chains
REVERT: C  346 ARG cc_start: 0.7633 (tpt90) cc_final: 0.7232 (tpt90)
REVERT: C  351 TYR cc_start: 0.8338 (p90) cc_final: 0.8090 (p90)
REVERT: C  395 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8472 (m)
REVERT: C  399 SER cc_start: 0.8689 (m) cc_final: 0.8437 (p)
REVERT: C  407 VAL cc_start: 0.8771 (t) cc_final: 0.8567 (p)
REVERT: C  429 PHE cc_start: 0.7878 (t80) cc_final: 0.7558 (t80)
REVERT: C  438 SER cc_start: 0.8727 (p) cc_final: 0.8460 (p)
REVERT: C  445 VAL cc_start: 0.8651 (t) cc_final: 0.8437 (m)
REVERT: C  456 PHE cc_start: 0.7620 (m-80) cc_final: 0.7416 (m-80)
REVERT: C  473 TYR cc_start: 0.6982 (t80) cc_final: 0.6615 (t80)
REVERT: C  494 SER cc_start: 0.8526 (t) cc_final: 0.8308 (p)
REVERT: A   18 LEU cc_start: 0.7877 (mt) cc_final: 0.7377 (mp)
REVERT: A   41 GLN cc_start: 0.8350 (tt0) cc_final: 0.8002 (tt0)
REVERT: A   52 LEU cc_start: 0.9002 (tp) cc_final: 0.8762 (tp)
REVERT: A   92 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8636 (p)
REVERT: A  107 PHE cc_start: 0.8236 (m-10) cc_final: 0.7979 (m-10)
REVERT: B   20 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7682 (mm)
REVERT: B   55 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6972 (mptp)
REVERT: B   63 ARG cc_start: 0.8586 (mtp180) cc_final: 0.8325 (mtp180)
REVERT: B   83 GLU cc_start: 0.7917 (mp0) cc_final: 0.7483 (mp0)
  outliers start: 18
  outliers final: 7
  residues processed: 112
  average time/residue: 0.4583
  time to fit residues: 54.8004
Evaluate side-chains
  103 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  528 LYS
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   55 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    0.0370
   chunk 13 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 34 optimal weight:    0.2980
   chunk 28 optimal weight:    0.2980
   chunk 32 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0670
   chunk 0 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0370
   overall best weight:    0.1474

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 506 GLN
A  78 ASN
B  33 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.134851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.123545 restraints weight = 5095.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 2.39
r_work: 0.3536 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3382 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3395  Z= 0.106
  Angle     :  0.577   9.872   4631  Z= 0.280
  Chirality :  0.043   0.223    516
  Planarity :  0.005   0.054    590
  Dihedral  :  5.367  42.745    477
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 16.39 %
    Favored  : 79.51 %
  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: -3.03 (0.39), residues: 422
  helix: -4.99 (0.27), residues: 20
  sheet: -0.98 (0.42), residues: 142
  loop : -2.49 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 436 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.021   0.001   PHE A  24 
 TYR   0.017   0.001   TYR B  51 
 ARG   0.002   0.000   ARG C 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02950 (   77)
  hydrogen bonds       : angle       6.27569 (  177)
  SS BOND              : bond        0.00319 (    6)
  SS BOND              : angle       0.60051 (   12)
  covalent geometry    : bond        0.00233 ( 3389)
  covalent geometry    : angle       0.57655 ( 4619)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.341 
Fit side-chains
REVERT: C  395 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8494 (m)
REVERT: C  396 TYR cc_start: 0.7892 (m-10) cc_final: 0.7594 (m-80)
REVERT: C  399 SER cc_start: 0.8701 (m) cc_final: 0.8499 (p)
REVERT: C  407 VAL cc_start: 0.8734 (t) cc_final: 0.8516 (p)
REVERT: C  429 PHE cc_start: 0.7885 (t80) cc_final: 0.7576 (t80)
REVERT: C  438 SER cc_start: 0.8654 (p) cc_final: 0.8372 (p)
REVERT: C  445 VAL cc_start: 0.8689 (t) cc_final: 0.8470 (m)
REVERT: C  456 PHE cc_start: 0.7602 (m-80) cc_final: 0.7337 (m-80)
REVERT: C  473 TYR cc_start: 0.6970 (t80) cc_final: 0.6712 (t80)
REVERT: C  494 SER cc_start: 0.8481 (t) cc_final: 0.8240 (p)
REVERT: C  511 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.8102 (t)
REVERT: A   18 LEU cc_start: 0.7645 (mt) cc_final: 0.7157 (mp)
REVERT: A   52 LEU cc_start: 0.8966 (tp) cc_final: 0.8763 (tp)
REVERT: B   55 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6767 (mptp)
REVERT: B   83 GLU cc_start: 0.7796 (mp0) cc_final: 0.7350 (mp0)
  outliers start: 15
  outliers final: 8
  residues processed: 101
  average time/residue: 0.5463
  time to fit residues: 58.6238
Evaluate side-chains
  110 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   55 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 25 optimal weight:    0.4980
   chunk 5 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0970
   chunk 22 optimal weight:    0.6980
   chunk 9 optimal weight:    0.3980
   chunk 19 optimal weight:    0.2980
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 506 GLN
A  78 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.131219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.119742 restraints weight = 5148.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 2.37
r_work: 0.3499 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   3395  Z= 0.190
  Angle     :  0.623  10.975   4631  Z= 0.300
  Chirality :  0.043   0.191    516
  Planarity :  0.005   0.058    590
  Dihedral  :  5.556  43.647    477
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.72 %
    Favored  : 90.28 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 17.49 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.40), residues: 422
  helix: -5.12 (0.26), residues: 12
  sheet: -0.84 (0.42), residues: 143
  loop : -2.28 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  49 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.019   0.001   PHE A  24 
 TYR   0.015   0.001   TYR B  51 
 ARG   0.001   0.000   ARG C 408 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03228 (   77)
  hydrogen bonds       : angle       6.20354 (  177)
  SS BOND              : bond        0.00325 (    6)
  SS BOND              : angle       0.94233 (   12)
  covalent geometry    : bond        0.00427 ( 3389)
  covalent geometry    : angle       0.62189 ( 4619)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.358 
Fit side-chains
REVERT: C  351 TYR cc_start: 0.8325 (p90) cc_final: 0.8046 (p90)
REVERT: C  395 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8488 (m)
REVERT: C  407 VAL cc_start: 0.8748 (t) cc_final: 0.8529 (p)
REVERT: C  429 PHE cc_start: 0.7953 (t80) cc_final: 0.7655 (t80)
REVERT: C  438 SER cc_start: 0.8696 (p) cc_final: 0.8409 (p)
REVERT: C  445 VAL cc_start: 0.8657 (t) cc_final: 0.8440 (m)
REVERT: C  456 PHE cc_start: 0.7654 (m-80) cc_final: 0.7405 (m-80)
REVERT: C  473 TYR cc_start: 0.7036 (t80) cc_final: 0.6835 (t80)
REVERT: C  494 SER cc_start: 0.8558 (t) cc_final: 0.8346 (p)
REVERT: C  511 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8161 (t)
REVERT: A   18 LEU cc_start: 0.7922 (mt) cc_final: 0.7387 (mp)
REVERT: A   52 LEU cc_start: 0.9014 (tp) cc_final: 0.8800 (tp)
REVERT: A   92 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8608 (p)
REVERT: B   20 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7748 (mm)
REVERT: B   55 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7047 (mptp)
REVERT: B   63 ARG cc_start: 0.8613 (mtp180) cc_final: 0.8265 (mtp180)
REVERT: B   83 GLU cc_start: 0.8070 (mp0) cc_final: 0.7528 (mp0)
  outliers start: 16
  outliers final: 7
  residues processed: 109
  average time/residue: 0.5004
  time to fit residues: 58.2115
Evaluate side-chains
  113 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  511 VAL
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   20 ILE
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   55 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 10 optimal weight:    0.0870
   chunk 16 optimal weight:    0.0870
   chunk 17 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0010
   chunk 37 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 25 optimal weight:    0.2980
   chunk 14 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0370
   overall best weight:    0.1020

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 414 GLN
C 450 ASN
C 506 GLN
A  78 ASN
B  40 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.134532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.123156 restraints weight = 5161.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 2.36
r_work: 0.3539 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3395  Z= 0.090
  Angle     :  0.571  10.178   4631  Z= 0.270
  Chirality :  0.042   0.206    516
  Planarity :  0.004   0.055    590
  Dihedral  :  5.015  36.395    475
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 18.58 %
    Favored  : 77.87 %
  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: -2.57 (0.40), residues: 422
  helix: -4.89 (0.29), residues: 20
  sheet: -0.71 (0.41), residues: 150
  loop : -2.14 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 436 
 HIS   0.000   0.000   HIS B  41 
 PHE   0.008   0.001   PHE C 400 
 TYR   0.015   0.001   TYR B  51 
 ARG   0.001   0.000   ARG C 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02567 (   77)
  hydrogen bonds       : angle       5.88580 (  177)
  SS BOND              : bond        0.00133 (    6)
  SS BOND              : angle       0.58302 (   12)
  covalent geometry    : bond        0.00195 ( 3389)
  covalent geometry    : angle       0.57052 ( 4619)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.327 
Fit side-chains
REVERT: C  392 PHE cc_start: 0.8361 (m-80) cc_final: 0.8061 (m-80)
REVERT: C  395 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8476 (m)
REVERT: C  396 TYR cc_start: 0.7889 (m-10) cc_final: 0.7562 (m-80)
REVERT: C  407 VAL cc_start: 0.8756 (t) cc_final: 0.8519 (p)
REVERT: C  429 PHE cc_start: 0.7920 (t80) cc_final: 0.7559 (t80)
REVERT: C  438 SER cc_start: 0.8619 (p) cc_final: 0.8311 (p)
REVERT: C  445 VAL cc_start: 0.8715 (t) cc_final: 0.8488 (m)
REVERT: C  456 PHE cc_start: 0.7645 (m-80) cc_final: 0.7385 (m-80)
REVERT: C  494 SER cc_start: 0.8439 (t) cc_final: 0.8201 (p)
REVERT: A   24 PHE cc_start: 0.8649 (p90) cc_final: 0.8436 (p90)
REVERT: A   96 TYR cc_start: 0.8556 (m-80) cc_final: 0.8352 (m-80)
REVERT: B   50 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8066 (pt)
REVERT: B   55 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6838 (mptp)
REVERT: B   63 ARG cc_start: 0.8553 (mtp180) cc_final: 0.8067 (mtp180)
REVERT: B   83 GLU cc_start: 0.7862 (mp0) cc_final: 0.7318 (mp0)
  outliers start: 13
  outliers final: 5
  residues processed: 104
  average time/residue: 0.4693
  time to fit residues: 52.1874
Evaluate side-chains
  103 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   55 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 15 optimal weight:    0.0980
   chunk 0 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 2 optimal weight:    0.4980
   chunk 30 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0980
   chunk 1 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 414 GLN
C 506 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.130199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.118477 restraints weight = 5244.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 2.38
r_work: 0.3486 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.2971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   3395  Z= 0.217
  Angle     :  0.652  12.103   4631  Z= 0.311
  Chirality :  0.044   0.208    516
  Planarity :  0.005   0.058    590
  Dihedral  :  5.294  33.051    475
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.48 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 21.58 %
    Favored  : 74.59 %
  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: -2.31 (0.40), residues: 422
  helix: -5.02 (0.31), residues: 12
  sheet: -0.50 (0.43), residues: 139
  loop : -2.04 (0.38), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  49 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.008   0.001   PHE A 107 
 TYR   0.018   0.002   TYR C 380 
 ARG   0.002   0.000   ARG C 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03245 (   77)
  hydrogen bonds       : angle       6.16635 (  177)
  SS BOND              : bond        0.00401 (    6)
  SS BOND              : angle       1.07617 (   12)
  covalent geometry    : bond        0.00483 ( 3389)
  covalent geometry    : angle       0.65042 ( 4619)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.362 
Fit side-chains
REVERT: C  395 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8487 (m)
REVERT: C  407 VAL cc_start: 0.8779 (t) cc_final: 0.8550 (p)
REVERT: C  429 PHE cc_start: 0.7971 (t80) cc_final: 0.7582 (t80)
REVERT: C  438 SER cc_start: 0.8671 (p) cc_final: 0.8410 (p)
REVERT: C  445 VAL cc_start: 0.8660 (t) cc_final: 0.8435 (m)
REVERT: C  473 TYR cc_start: 0.6896 (t80) cc_final: 0.6420 (t80)
REVERT: C  494 SER cc_start: 0.8638 (t) cc_final: 0.8390 (p)
REVERT: C  503 VAL cc_start: 0.8631 (t) cc_final: 0.8215 (p)
REVERT: C  512 VAL cc_start: 0.8505 (m) cc_final: 0.8189 (p)
REVERT: A   29 LEU cc_start: 0.8616 (tp) cc_final: 0.8401 (tt)
REVERT: A   92 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8632 (p)
REVERT: B   55 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7104 (mptp)
REVERT: B   63 ARG cc_start: 0.8619 (mtp180) cc_final: 0.8334 (mtp180)
REVERT: B   83 GLU cc_start: 0.8125 (mp0) cc_final: 0.7560 (mp0)
  outliers start: 14
  outliers final: 9
  residues processed: 113
  average time/residue: 0.5023
  time to fit residues: 60.6296
Evaluate side-chains
  115 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   55 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    0.4980
   chunk 13 optimal weight:    0.0970
   chunk 15 optimal weight:    0.0980
   chunk 38 optimal weight:    0.9980
   chunk 16 optimal weight:    0.4980
   chunk 23 optimal weight:    0.3980
   chunk 17 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 28 optimal weight:    0.2980
   chunk 7 optimal weight:    0.5980
   chunk 1 optimal weight:    0.3980
   overall best weight:    0.2578

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 414 GLN
C 450 ASN
C 506 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.131374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.120081 restraints weight = 5121.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 2.33
r_work: 0.3505 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.3014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3395  Z= 0.136
  Angle     :  0.636  11.824   4631  Z= 0.295
  Chirality :  0.043   0.204    516
  Planarity :  0.005   0.056    590
  Dihedral  :  5.285  37.964    475
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 22.40 %
    Favored  : 74.04 %
  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: -2.12 (0.41), residues: 422
  helix: -5.00 (0.33), residues: 12
  sheet: -0.36 (0.44), residues: 139
  loop : -1.91 (0.39), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 436 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.011   0.001   PHE C 456 
 TYR   0.014   0.001   TYR C 380 
 ARG   0.001   0.000   ARG C 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02891 (   77)
  hydrogen bonds       : angle       6.00315 (  177)
  SS BOND              : bond        0.00235 (    6)
  SS BOND              : angle       0.81417 (   12)
  covalent geometry    : bond        0.00306 ( 3389)
  covalent geometry    : angle       0.63531 ( 4619)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.318 
Fit side-chains
REVERT: C  367 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7844 (m)
REVERT: C  395 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8478 (m)
REVERT: C  407 VAL cc_start: 0.8764 (t) cc_final: 0.8525 (p)
REVERT: C  429 PHE cc_start: 0.7964 (t80) cc_final: 0.7595 (t80)
REVERT: C  438 SER cc_start: 0.8639 (p) cc_final: 0.8327 (p)
REVERT: C  445 VAL cc_start: 0.8663 (t) cc_final: 0.8455 (m)
REVERT: C  473 TYR cc_start: 0.6863 (t80) cc_final: 0.6448 (t80)
REVERT: C  494 SER cc_start: 0.8586 (t) cc_final: 0.8337 (p)
REVERT: C  503 VAL cc_start: 0.8571 (t) cc_final: 0.8141 (p)
REVERT: C  523 THR cc_start: 0.8048 (p) cc_final: 0.7705 (t)
REVERT: A   29 LEU cc_start: 0.8610 (tp) cc_final: 0.8387 (tt)
REVERT: A   31 THR cc_start: 0.8765 (m) cc_final: 0.8334 (p)
REVERT: A   92 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8659 (p)
REVERT: B   55 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7000 (mptp)
REVERT: B   63 ARG cc_start: 0.8588 (mtp180) cc_final: 0.8324 (mtp180)
REVERT: B   83 GLU cc_start: 0.7994 (mp0) cc_final: 0.7413 (mp0)
  outliers start: 13
  outliers final: 6
  residues processed: 121
  average time/residue: 0.5716
  time to fit residues: 74.5403
Evaluate side-chains
  115 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   55 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 506 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.128491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.116933 restraints weight = 5191.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 2.37
r_work: 0.3454 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.3373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.083   3395  Z= 0.321
  Angle     :  0.743  13.188   4631  Z= 0.357
  Chirality :  0.047   0.221    516
  Planarity :  0.005   0.060    590
  Dihedral  :  5.756  33.721    475
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.09 %
    Favored  : 87.91 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 22.95 %
    Favored  : 72.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -2.28 (0.41), residues: 422
  helix: -4.99 (0.33), residues: 12
  sheet: -0.61 (0.42), residues: 151
  loop : -1.99 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  49 
 HIS   0.001   0.001   HIS C 505 
 PHE   0.009   0.002   PHE A 107 
 TYR   0.021   0.002   TYR C 380 
 ARG   0.004   0.001   ARG C 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03831 (   77)
  hydrogen bonds       : angle       6.42939 (  177)
  SS BOND              : bond        0.00527 (    6)
  SS BOND              : angle       1.36540 (   12)
  covalent geometry    : bond        0.00725 ( 3389)
  covalent geometry    : angle       0.74112 ( 4619)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.689 
Fit side-chains
REVERT: C  357 ARG cc_start: 0.7989 (ptp-110) cc_final: 0.7748 (ptp-110)
REVERT: C  367 VAL cc_start: 0.8107 (OUTLIER) cc_final: 0.7899 (m)
REVERT: C  395 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8462 (m)
REVERT: C  407 VAL cc_start: 0.8790 (t) cc_final: 0.8563 (p)
REVERT: C  429 PHE cc_start: 0.8041 (t80) cc_final: 0.7668 (t80)
REVERT: C  438 SER cc_start: 0.8690 (p) cc_final: 0.8419 (p)
REVERT: C  445 VAL cc_start: 0.8680 (t) cc_final: 0.8468 (m)
REVERT: C  473 TYR cc_start: 0.6929 (t80) cc_final: 0.6469 (t80)
REVERT: C  503 VAL cc_start: 0.8747 (t) cc_final: 0.8352 (p)
REVERT: C  512 VAL cc_start: 0.8525 (m) cc_final: 0.8220 (p)
REVERT: A   10 THR cc_start: 0.8672 (p) cc_final: 0.8270 (t)
REVERT: A   31 THR cc_start: 0.8723 (m) cc_final: 0.8248 (p)
REVERT: B   55 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7152 (mptp)
REVERT: B   83 GLU cc_start: 0.8219 (mp0) cc_final: 0.7638 (mp0)
  outliers start: 15
  outliers final: 9
  residues processed: 118
  average time/residue: 0.6484
  time to fit residues: 82.5378
Evaluate side-chains
  122 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   55 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 22 optimal weight:    0.3980
   chunk 1 optimal weight:    0.3980
   chunk 17 optimal weight:    0.1980
   chunk 5 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 36 optimal weight:    0.3980
   chunk 35 optimal weight:    0.2980
   overall best weight:    0.3380

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 450 ASN
A  86 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.129986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.118724 restraints weight = 5126.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 2.32
r_work: 0.3488 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3333 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.3338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3395  Z= 0.173
  Angle     :  0.685  12.657   4631  Z= 0.320
  Chirality :  0.045   0.213    516
  Planarity :  0.005   0.057    590
  Dihedral  :  5.562  42.408    474
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 23.22 %
    Favored  : 72.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -2.12 (0.41), residues: 422
  helix: -4.98 (0.34), residues: 12
  sheet: -0.51 (0.42), residues: 151
  loop : -1.86 (0.39), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 436 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.015   0.001   PHE A  24 
 TYR   0.016   0.002   TYR C 380 
 ARG   0.002   0.000   ARG C 408 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03178 (   77)
  hydrogen bonds       : angle       6.25322 (  177)
  SS BOND              : bond        0.00272 (    6)
  SS BOND              : angle       0.90508 (   12)
  covalent geometry    : bond        0.00394 ( 3389)
  covalent geometry    : angle       0.68459 ( 4619)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 1.130 
Fit side-chains
REVERT: C  357 ARG cc_start: 0.7944 (ptp-110) cc_final: 0.7708 (ptp-110)
REVERT: C  367 VAL cc_start: 0.8016 (OUTLIER) cc_final: 0.7808 (m)
REVERT: C  392 PHE cc_start: 0.8538 (m-80) cc_final: 0.8182 (m-80)
REVERT: C  395 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8447 (m)
REVERT: C  407 VAL cc_start: 0.8770 (t) cc_final: 0.8541 (p)
REVERT: C  429 PHE cc_start: 0.8037 (t80) cc_final: 0.7617 (t80)
REVERT: C  438 SER cc_start: 0.8652 (p) cc_final: 0.8367 (p)
REVERT: C  445 VAL cc_start: 0.8667 (t) cc_final: 0.8452 (m)
REVERT: C  473 TYR cc_start: 0.6814 (t80) cc_final: 0.6422 (t80)
REVERT: C  503 VAL cc_start: 0.8628 (t) cc_final: 0.8213 (p)
REVERT: C  512 VAL cc_start: 0.8544 (m) cc_final: 0.8219 (p)
REVERT: C  523 THR cc_start: 0.8102 (p) cc_final: 0.7715 (t)
REVERT: A   29 LEU cc_start: 0.8676 (tp) cc_final: 0.8447 (tt)
REVERT: A   31 THR cc_start: 0.8739 (m) cc_final: 0.8284 (p)
REVERT: A   92 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8612 (p)
REVERT: B   55 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7081 (mptp)
REVERT: B   83 GLU cc_start: 0.8105 (mp0) cc_final: 0.7501 (mp0)
  outliers start: 14
  outliers final: 8
  residues processed: 121
  average time/residue: 0.8333
  time to fit residues: 109.3953
Evaluate side-chains
  121 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   55 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 10 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0980
   chunk 8 optimal weight:    0.4980
   chunk 13 optimal weight:    0.3980
   chunk 15 optimal weight:    0.0040
   chunk 5 optimal weight:    0.2980
   chunk 7 optimal weight:    0.4980
   chunk 27 optimal weight:    0.7980
   chunk 25 optimal weight:    0.4980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.2592

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 450 ASN
C 506 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.131965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.120767 restraints weight = 5062.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.29
r_work: 0.3494 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.3419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3395  Z= 0.142
  Angle     :  0.667  12.689   4631  Z= 0.311
  Chirality :  0.044   0.187    516
  Planarity :  0.005   0.057    590
  Dihedral  :  5.349  39.790    474
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 24.59 %
    Favored  : 72.13 %
  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: -1.97 (0.41), residues: 422
  helix: -4.97 (0.35), residues: 12
  sheet: -0.43 (0.42), residues: 152
  loop : -1.73 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 436 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.008   0.001   PHE A 107 
 TYR   0.016   0.001   TYR C 421 
 ARG   0.003   0.000   ARG B  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02962 (   77)
  hydrogen bonds       : angle       6.11552 (  177)
  SS BOND              : bond        0.00238 (    6)
  SS BOND              : angle       0.87184 (   12)
  covalent geometry    : bond        0.00323 ( 3389)
  covalent geometry    : angle       0.66624 ( 4619)

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: C  357 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7677 (ptp-110)
REVERT: C  392 PHE cc_start: 0.8486 (m-80) cc_final: 0.8076 (m-80)
REVERT: C  407 VAL cc_start: 0.8786 (t) cc_final: 0.8570 (p)
REVERT: C  429 PHE cc_start: 0.8006 (t80) cc_final: 0.7664 (t80)
REVERT: C  438 SER cc_start: 0.8637 (p) cc_final: 0.8316 (p)
REVERT: C  445 VAL cc_start: 0.8676 (t) cc_final: 0.8469 (m)
REVERT: C  473 TYR cc_start: 0.6800 (t80) cc_final: 0.6452 (t80)
REVERT: C  503 VAL cc_start: 0.8585 (t) cc_final: 0.8172 (p)
REVERT: C  523 THR cc_start: 0.8057 (p) cc_final: 0.7663 (t)
REVERT: A   24 PHE cc_start: 0.8648 (p90) cc_final: 0.8137 (p90)
REVERT: A   31 THR cc_start: 0.8728 (m) cc_final: 0.8287 (p)
REVERT: A   92 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8594 (p)
REVERT: B   55 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.6956 (mptp)
REVERT: B   83 GLU cc_start: 0.8085 (mp0) cc_final: 0.7472 (mp0)
  outliers start: 12
  outliers final: 7
  residues processed: 113
  average time/residue: 0.4868
  time to fit residues: 59.0294
Evaluate side-chains
  116 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  357 ARG
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain B residue   55 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0370
   chunk 29 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0020
   chunk 16 optimal weight:    0.1980
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.3266

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 506 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.131695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.120226 restraints weight = 5155.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 2.39
r_work: 0.3488 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.3440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3395  Z= 0.166
  Angle     :  0.684  13.167   4631  Z= 0.319
  Chirality :  0.044   0.183    516
  Planarity :  0.005   0.057    590
  Dihedral  :  5.190  41.626    471
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.95 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 24.86 %
    Favored  : 72.40 %
  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: -1.92 (0.41), residues: 422
  helix: -4.97 (0.35), residues: 12
  sheet: -0.40 (0.42), residues: 152
  loop : -1.69 (0.40), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 436 
 HIS   0.001   0.000   HIS B  41 
 PHE   0.013   0.001   PHE C 400 
 TYR   0.015   0.002   TYR C 421 
 ARG   0.004   0.000   ARG B  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03243 (   77)
  hydrogen bonds       : angle       6.08473 (  177)
  SS BOND              : bond        0.00275 (    6)
  SS BOND              : angle       0.99382 (   12)
  covalent geometry    : bond        0.00377 ( 3389)
  covalent geometry    : angle       0.68303 ( 4619)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3853.58 seconds
wall clock time: 70 minutes 0.05 seconds (4200.05 seconds total)