Starting phenix.real_space_refine
on Tue Mar  3 11:31:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yd1_33745/03_2026/7yd1_33745.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yd1_33745/03_2026/7yd1_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yd1_33745/03_2026/7yd1_33745.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yd1_33745/03_2026/7yd1_33745.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yd1_33745/03_2026/7yd1_33745.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yd1_33745/03_2026/7yd1_33745.map"
  }
  resolution = 2.99
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.011
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.86, per 1000 atoms: 0.26
  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: 0.21
  Conformation dependent library (CDL) restraints added in 130.0 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: 0.09
  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: 0.37

  Time building geometry restraints manager: 0.30 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:             2.380
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.010
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.100
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.06 (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
 ARG   0.002   0.000   ARG C 457 
 TYR   0.018   0.001   TYR B  51 
 PHE   0.007   0.001   PHE C 429 
 TRP   0.007   0.001   TRP C 436 
 HIS   0.000   0.000   HIS B  41 

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

*********************** 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  : 0.119 
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: 0.8316 (m) cc_final: 0.7940 (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: 0.8449 (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: 0.6209 (m-80)
REVERT: C  494 SER cc_start: 0.8374 (t) cc_final: 0.8151 (p)
REVERT: C  515 PHE cc_start: 0.8610 (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: 0.8404 (mt) cc_final: 0.8121 (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: 0.7756 (m-80)
REVERT: A   87 MET cc_start: 0.6148 (mmm) cc_final: 0.5526 (mmm)
REVERT: A  107 PHE cc_start: 0.8136 (m-10) cc_final: 0.7886 (m-10)
REVERT: A  112 GLN cc_start: 0.6422 (pp30) cc_final: 0.6128 (pp30)
  outliers start: 20
  outliers final: 5
  residues processed: 124
  average time/residue: 0.2224
  time to fit residues: 29.2939
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  : 0.119 
-------------------------------------------------------------------------------
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 24 optimal weight:    0.4980
   chunk 26 optimal weight:    0.0370
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.5458

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  81 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.132801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.121197 restraints weight = 5106.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 2.36
r_work: 0.3503 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3344 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066   3395  Z= 0.250
  Angle     :  0.657  11.683   4631  Z= 0.329
  Chirality :  0.045   0.205    516
  Planarity :  0.005   0.059    590
  Dihedral  :  5.842  45.315    479
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.09 %
    Favored  : 87.91 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.39 (0.38), residues: 422
  helix: -5.23 (0.23), residues: 12
  sheet: -1.45 (0.41), residues: 146
  loop : -2.70 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 457 
 TYR   0.016   0.002   TYR B  51 
 PHE   0.011   0.001   PHE A  24 
 TRP   0.018   0.002   TRP A  49 
 HIS   0.001   0.000   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00556 ( 3389)
  covalent geometry    : angle       0.65660 ( 4619)
  SS BOND              : bond        0.00334 (    6)
  SS BOND              : angle       0.75515 (   12)
  hydrogen bonds       : bond        0.03944 (   77)
  hydrogen bonds       : angle       6.76026 (  177)

*********************** 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
  122 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.164 
Fit side-chains
REVERT: C  346 ARG cc_start: 0.7645 (tpt90) cc_final: 0.7235 (tpt90)
REVERT: C  351 TYR cc_start: 0.8342 (p90) cc_final: 0.8105 (p90)
REVERT: C  395 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8475 (m)
REVERT: C  399 SER cc_start: 0.8706 (m) cc_final: 0.8467 (p)
REVERT: C  407 VAL cc_start: 0.8774 (t) cc_final: 0.8566 (p)
REVERT: C  429 PHE cc_start: 0.7890 (t80) cc_final: 0.7599 (t80)
REVERT: C  438 SER cc_start: 0.8729 (p) cc_final: 0.8467 (p)
REVERT: C  456 PHE cc_start: 0.7634 (m-80) cc_final: 0.7428 (m-80)
REVERT: C  473 TYR cc_start: 0.6980 (t80) cc_final: 0.6607 (t80)
REVERT: C  494 SER cc_start: 0.8542 (t) cc_final: 0.8321 (p)
REVERT: A   18 LEU cc_start: 0.7937 (mt) cc_final: 0.7418 (mp)
REVERT: A   41 GLN cc_start: 0.8362 (tt0) cc_final: 0.8021 (tt0)
REVERT: A   52 LEU cc_start: 0.9006 (tp) cc_final: 0.8787 (tp)
REVERT: A   92 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8642 (p)
REVERT: A  107 PHE cc_start: 0.8242 (m-10) cc_final: 0.7989 (m-10)
REVERT: B   20 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7693 (mm)
REVERT: B   55 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6987 (mptp)
REVERT: B   63 ARG cc_start: 0.8591 (mtp180) cc_final: 0.8329 (mtp180)
REVERT: B   83 GLU cc_start: 0.7940 (mp0) cc_final: 0.7505 (mp0)
  outliers start: 18
  outliers final: 8
  residues processed: 111
  average time/residue: 0.2231
  time to fit residues: 26.3833
Evaluate side-chains
  111 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
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  470 THR
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 7 optimal weight:    0.4980
   chunk 28 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0370
   chunk 11 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0770
   chunk 5 optimal weight:    0.5980
   chunk 34 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.3416

-------------------------------------------------------------------------------
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
B  39 GLN
B  41 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.132447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.121102 restraints weight = 5155.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 2.37
r_work: 0.3508 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3395  Z= 0.168
  Angle     :  0.620  10.503   4631  Z= 0.301
  Chirality :  0.044   0.235    516
  Planarity :  0.005   0.057    590
  Dihedral  :  5.608  43.854    477
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 15.03 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.00 (0.39), residues: 422
  helix: -5.17 (0.25), residues: 12
  sheet: -1.19 (0.41), residues: 146
  loop : -2.43 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 457 
 TYR   0.015   0.001   TYR B  51 
 PHE   0.021   0.001   PHE A  24 
 TRP   0.013   0.001   TRP C 436 
 HIS   0.001   0.000   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 3389)
  covalent geometry    : angle       0.62018 ( 4619)
  SS BOND              : bond        0.00320 (    6)
  SS BOND              : angle       0.65413 (   12)
  hydrogen bonds       : bond        0.03301 (   77)
  hydrogen bonds       : angle       6.40971 (  177)

*********************** 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
  118 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.117 
Fit side-chains
REVERT: C  351 TYR cc_start: 0.8339 (p90) cc_final: 0.8070 (p90)
REVERT: C  392 PHE cc_start: 0.8505 (m-80) cc_final: 0.7996 (m-80)
REVERT: C  395 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8485 (m)
REVERT: C  407 VAL cc_start: 0.8748 (t) cc_final: 0.8525 (p)
REVERT: C  429 PHE cc_start: 0.7926 (t80) cc_final: 0.7577 (t80)
REVERT: C  438 SER cc_start: 0.8697 (p) cc_final: 0.8419 (p)
REVERT: C  456 PHE cc_start: 0.7641 (m-80) cc_final: 0.7390 (m-80)
REVERT: C  473 TYR cc_start: 0.6998 (t80) cc_final: 0.6738 (t80)
REVERT: C  494 SER cc_start: 0.8549 (t) cc_final: 0.8334 (p)
REVERT: C  512 VAL cc_start: 0.8528 (m) cc_final: 0.8202 (p)
REVERT: A   18 LEU cc_start: 0.7786 (mt) cc_final: 0.7273 (mp)
REVERT: A   52 LEU cc_start: 0.9007 (tp) cc_final: 0.8768 (tp)
REVERT: A   92 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8582 (p)
REVERT: A  107 PHE cc_start: 0.8256 (m-10) cc_final: 0.8006 (m-10)
REVERT: B   50 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8119 (pt)
REVERT: B   55 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.6946 (mptp)
REVERT: B   83 GLU cc_start: 0.7965 (mp0) cc_final: 0.7503 (mp0)
  outliers start: 19
  outliers final: 9
  residues processed: 108
  average time/residue: 0.2340
  time to fit residues: 26.7891
Evaluate side-chains
  115 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
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  382 VAL
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   50 ILE
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 20 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0570
   chunk 35 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0980
   chunk 28 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.4098

-------------------------------------------------------------------------------
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
A  78 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.130662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.119222 restraints weight = 5132.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 2.36
r_work: 0.3485 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3327 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   3395  Z= 0.194
  Angle     :  0.625  10.686   4631  Z= 0.303
  Chirality :  0.044   0.220    516
  Planarity :  0.005   0.062    590
  Dihedral  :  5.656  43.343    477
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.95 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 17.76 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.77 (0.40), residues: 422
  helix: -5.14 (0.26), residues: 12
  sheet: -0.99 (0.42), residues: 144
  loop : -2.28 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  60 
 TYR   0.014   0.001   TYR B  51 
 PHE   0.019   0.001   PHE A  24 
 TRP   0.013   0.002   TRP C 436 
 HIS   0.001   0.000   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 3389)
  covalent geometry    : angle       0.62400 ( 4619)
  SS BOND              : bond        0.00350 (    6)
  SS BOND              : angle       0.82045 (   12)
  hydrogen bonds       : bond        0.03323 (   77)
  hydrogen bonds       : angle       6.22538 (  177)

*********************** 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
  120 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.130 
Fit side-chains
REVERT: C  341 VAL cc_start: 0.8854 (m) cc_final: 0.8643 (p)
REVERT: C  395 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8470 (m)
REVERT: C  407 VAL cc_start: 0.8766 (t) cc_final: 0.8536 (p)
REVERT: C  429 PHE cc_start: 0.7939 (t80) cc_final: 0.7691 (t80)
REVERT: C  438 SER cc_start: 0.8688 (p) cc_final: 0.8391 (p)
REVERT: C  445 VAL cc_start: 0.8645 (t) cc_final: 0.8412 (m)
REVERT: C  456 PHE cc_start: 0.7675 (m-80) cc_final: 0.7433 (m-80)
REVERT: C  494 SER cc_start: 0.8608 (t) cc_final: 0.8367 (p)
REVERT: C  503 VAL cc_start: 0.8593 (t) cc_final: 0.8183 (p)
REVERT: C  512 VAL cc_start: 0.8477 (m) cc_final: 0.8164 (p)
REVERT: A   52 LEU cc_start: 0.9022 (tp) cc_final: 0.8780 (tp)
REVERT: A   92 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8608 (p)
REVERT: A  107 PHE cc_start: 0.8286 (m-10) cc_final: 0.8070 (m-10)
REVERT: B   55 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7254 (mptp)
REVERT: B   83 GLU cc_start: 0.8113 (mp0) cc_final: 0.7548 (mp0)
  outliers start: 18
  outliers final: 8
  residues processed: 112
  average time/residue: 0.2309
  time to fit residues: 27.5707
Evaluate side-chains
  112 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
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  382 VAL
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  395 VAL
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:    0.0870
   chunk 32 optimal weight:    0.1980
   chunk 6 optimal weight:    0.2980
   chunk 1 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.4980
   chunk 30 optimal weight:    0.3980
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.2758

-------------------------------------------------------------------------------
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
A  78 ASN
B  40 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.132380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.120996 restraints weight = 5165.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 2.37
r_work: 0.3504 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3347 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3395  Z= 0.145
  Angle     :  0.622  10.566   4631  Z= 0.295
  Chirality :  0.043   0.209    516
  Planarity :  0.005   0.058    590
  Dihedral  :  5.276  36.993    475
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 20.22 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.49 (0.40), residues: 422
  helix: -5.11 (0.27), residues: 12
  sheet: -0.73 (0.42), residues: 144
  loop : -2.12 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  60 
 TYR   0.014   0.001   TYR B  51 
 PHE   0.032   0.001   PHE C 342 
 TRP   0.011   0.001   TRP C 436 
 HIS   0.001   0.000   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 3389)
  covalent geometry    : angle       0.62118 ( 4619)
  SS BOND              : bond        0.00229 (    6)
  SS BOND              : angle       0.82818 (   12)
  hydrogen bonds       : bond        0.02981 (   77)
  hydrogen bonds       : angle       6.03006 (  177)

*********************** 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
  122 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.125 
Fit side-chains
REVERT: C  395 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8477 (m)
REVERT: C  407 VAL cc_start: 0.8760 (t) cc_final: 0.8531 (p)
REVERT: C  438 SER cc_start: 0.8668 (p) cc_final: 0.8358 (p)
REVERT: C  445 VAL cc_start: 0.8647 (t) cc_final: 0.8434 (m)
REVERT: C  456 PHE cc_start: 0.7665 (m-80) cc_final: 0.7456 (m-80)
REVERT: C  473 TYR cc_start: 0.6858 (t80) cc_final: 0.6453 (t80)
REVERT: C  494 SER cc_start: 0.8567 (t) cc_final: 0.8333 (p)
REVERT: C  503 VAL cc_start: 0.8580 (t) cc_final: 0.8149 (p)
REVERT: A   52 LEU cc_start: 0.9029 (tp) cc_final: 0.8798 (tp)
REVERT: A   92 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8621 (p)
REVERT: B   55 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7142 (mptp)
REVERT: B   63 ARG cc_start: 0.8606 (mtp180) cc_final: 0.8102 (mtp180)
REVERT: B   83 GLU cc_start: 0.8032 (mp0) cc_final: 0.7448 (mp0)
  outliers start: 15
  outliers final: 7
  residues processed: 117
  average time/residue: 0.2438
  time to fit residues: 30.2475
Evaluate side-chains
  114 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0030
   chunk 0 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0270
   chunk 35 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.5448

-------------------------------------------------------------------------------
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
A  78 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.129157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.117648 restraints weight = 5134.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 2.36
r_work: 0.3470 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.3158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067   3395  Z= 0.250
  Angle     :  0.677  12.092   4631  Z= 0.329
  Chirality :  0.045   0.211    516
  Planarity :  0.005   0.060    590
  Dihedral  :  5.576  33.954    475
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.14 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 21.31 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.47 (0.40), residues: 422
  helix: -5.09 (0.27), residues: 12
  sheet: -0.75 (0.43), residues: 146
  loop : -2.09 (0.39), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  60 
 TYR   0.016   0.002   TYR C 380 
 PHE   0.015   0.002   PHE A  24 
 TRP   0.016   0.002   TRP A  49 
 HIS   0.001   0.000   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 ( 3389)
  covalent geometry    : angle       0.67554 ( 4619)
  SS BOND              : bond        0.00385 (    6)
  SS BOND              : angle       1.15448 (   12)
  hydrogen bonds       : bond        0.03504 (   77)
  hydrogen bonds       : angle       6.20861 (  177)

*********************** 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
  115 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
REVERT: C  395 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8473 (m)
REVERT: C  407 VAL cc_start: 0.8795 (t) cc_final: 0.8551 (p)
REVERT: C  429 PHE cc_start: 0.8057 (t80) cc_final: 0.7799 (t80)
REVERT: C  438 SER cc_start: 0.8723 (p) cc_final: 0.8439 (p)
REVERT: C  445 VAL cc_start: 0.8679 (t) cc_final: 0.8451 (m)
REVERT: C  473 TYR cc_start: 0.6823 (t80) cc_final: 0.6403 (t80)
REVERT: C  503 VAL cc_start: 0.8670 (t) cc_final: 0.8282 (p)
REVERT: C  512 VAL cc_start: 0.8547 (m) cc_final: 0.8265 (p)
REVERT: A   52 LEU cc_start: 0.9020 (tp) cc_final: 0.8770 (tp)
REVERT: A   92 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8623 (p)
REVERT: B   55 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7172 (mptp)
REVERT: B   78 SER cc_start: 0.7937 (t) cc_final: 0.7450 (p)
REVERT: B   83 GLU cc_start: 0.8197 (mp0) cc_final: 0.7619 (mp0)
  outliers start: 16
  outliers final: 11
  residues processed: 109
  average time/residue: 0.2367
  time to fit residues: 27.4527
Evaluate side-chains
  106 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
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  382 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 C residue  470 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 28 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0980
   chunk 35 optimal weight:    0.5980
   chunk 8 optimal weight:    0.1980
   chunk 38 optimal weight:    0.0870
   chunk 21 optimal weight:    0.0870
   chunk 18 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.2136

-------------------------------------------------------------------------------
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 460 ASN
C 506 GLN
A  78 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.131285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.119848 restraints weight = 5222.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 2.38
r_work: 0.3501 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3347 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.3190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3395  Z= 0.125
  Angle     :  0.620  11.004   4631  Z= 0.294
  Chirality :  0.043   0.192    516
  Planarity :  0.004   0.056    590
  Dihedral  :  5.370  41.198    475
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 21.86 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.16 (0.41), residues: 422
  helix: -5.05 (0.30), residues: 12
  sheet: -0.47 (0.43), residues: 140
  loop : -1.88 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 357 
 TYR   0.014   0.001   TYR C 421 
 PHE   0.011   0.001   PHE C 456 
 TRP   0.012   0.001   TRP C 436 
 HIS   0.001   0.000   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 3389)
  covalent geometry    : angle       0.61977 ( 4619)
  SS BOND              : bond        0.00214 (    6)
  SS BOND              : angle       0.85142 (   12)
  hydrogen bonds       : bond        0.02825 (   77)
  hydrogen bonds       : angle       5.96560 (  177)

*********************** 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
  105 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  357 ARG cc_start: 0.7998 (ptp-110) cc_final: 0.7784 (ptp-110)
REVERT: C  395 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8457 (m)
REVERT: C  429 PHE cc_start: 0.8067 (t80) cc_final: 0.7728 (t80)
REVERT: C  438 SER cc_start: 0.8663 (p) cc_final: 0.8346 (p)
REVERT: C  445 VAL cc_start: 0.8695 (t) cc_final: 0.8476 (m)
REVERT: C  473 TYR cc_start: 0.6775 (t80) cc_final: 0.6398 (t80)
REVERT: C  494 SER cc_start: 0.8557 (t) cc_final: 0.8329 (p)
REVERT: C  523 THR cc_start: 0.8030 (p) cc_final: 0.7625 (t)
REVERT: A   92 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8638 (p)
REVERT: B   55 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7064 (mptp)
REVERT: B   83 GLU cc_start: 0.8046 (mp0) cc_final: 0.7455 (mp0)
  outliers start: 13
  outliers final: 7
  residues processed: 100
  average time/residue: 0.2603
  time to fit residues: 27.5360
Evaluate side-chains
  109 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0270
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.6038

-------------------------------------------------------------------------------
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 = 0.3742 r_free = 0.3742 target = 0.128841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.117677 restraints weight = 5190.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 2.31
r_work: 0.3460 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3303 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072   3395  Z= 0.274
  Angle     :  0.701  13.003   4631  Z= 0.339
  Chirality :  0.046   0.199    516
  Planarity :  0.005   0.060    590
  Dihedral  :  5.401  31.972    473
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.37 %
    Favored  : 88.63 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 22.95 %
    Favored  : 73.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.17 (0.41), residues: 422
  helix: -5.03 (0.31), residues: 12
  sheet: -0.52 (0.43), residues: 142
  loop : -1.87 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 509 
 TYR   0.017   0.002   TYR C 453 
 PHE   0.016   0.002   PHE A  24 
 TRP   0.016   0.002   TRP A  49 
 HIS   0.001   0.000   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00616 ( 3389)
  covalent geometry    : angle       0.69907 ( 4619)
  SS BOND              : bond        0.00398 (    6)
  SS BOND              : angle       1.30573 (   12)
  hydrogen bonds       : bond        0.03626 (   77)
  hydrogen bonds       : angle       6.14857 (  177)

*********************** 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
  114 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.079 
Fit side-chains
   revert: symmetry clash
REVERT: C  357 ARG cc_start: 0.7992 (ptp-110) cc_final: 0.7790 (ptp-110)
REVERT: C  429 PHE cc_start: 0.8120 (t80) cc_final: 0.7830 (t80)
REVERT: C  438 SER cc_start: 0.8712 (p) cc_final: 0.8437 (p)
REVERT: C  445 VAL cc_start: 0.8680 (t) cc_final: 0.8454 (m)
REVERT: C  473 TYR cc_start: 0.6811 (t80) cc_final: 0.6415 (t80)
REVERT: A   92 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8647 (p)
REVERT: B   55 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7138 (mptp)
REVERT: B   78 SER cc_start: 0.7929 (t) cc_final: 0.7446 (p)
REVERT: B   83 GLU cc_start: 0.8200 (mp0) cc_final: 0.7609 (mp0)
  outliers start: 12
  outliers final: 6
  residues processed: 110
  average time/residue: 0.2394
  time to fit residues: 27.9148
Evaluate side-chains
  107 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0470
   chunk 16 optimal weight:    0.4980
   chunk 36 optimal weight:    0.0570
   chunk 38 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.3596

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 460 ASN
C 506 GLN
A  78 ASN
A  86 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.130329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.119015 restraints weight = 5196.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.34
r_work: 0.3486 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3333 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.3388

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= 0.180
  Angle     :  0.686  12.726   4631  Z= 0.321
  Chirality :  0.045   0.189    516
  Planarity :  0.005   0.058    590
  Dihedral  :  5.250  32.563    472
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.48 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 22.40 %
    Favored  : 73.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.05 (0.41), residues: 422
  helix: -5.02 (0.32), residues: 12
  sheet: -0.46 (0.43), residues: 142
  loop : -1.77 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  63 
 TYR   0.015   0.001   TYR C 453 
 PHE   0.012   0.001   PHE C 400 
 TRP   0.013   0.001   TRP C 436 
 HIS   0.001   0.000   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 3389)
  covalent geometry    : angle       0.68417 ( 4619)
  SS BOND              : bond        0.00278 (    6)
  SS BOND              : angle       1.11828 (   12)
  hydrogen bonds       : bond        0.03259 (   77)
  hydrogen bonds       : angle       5.98753 (  177)

*********************** 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
  112 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  357 ARG cc_start: 0.7982 (ptp-110) cc_final: 0.7769 (ptp-110)
REVERT: C  429 PHE cc_start: 0.8111 (t80) cc_final: 0.7737 (t80)
REVERT: C  438 SER cc_start: 0.8687 (p) cc_final: 0.8378 (p)
REVERT: C  445 VAL cc_start: 0.8687 (t) cc_final: 0.8464 (m)
REVERT: C  473 TYR cc_start: 0.6786 (t80) cc_final: 0.6389 (t80)
REVERT: C  512 VAL cc_start: 0.8571 (m) cc_final: 0.8281 (p)
REVERT: C  523 THR cc_start: 0.8088 (p) cc_final: 0.7699 (t)
REVERT: A   92 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8646 (p)
REVERT: B   18 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7988 (pt)
REVERT: B   55 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7092 (mptp)
REVERT: B   78 SER cc_start: 0.7855 (t) cc_final: 0.7419 (p)
REVERT: B   83 GLU cc_start: 0.8140 (mp0) cc_final: 0.7540 (mp0)
  outliers start: 14
  outliers final: 7
  residues processed: 106
  average time/residue: 0.2176
  time to fit residues: 24.5976
Evaluate side-chains
  107 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  430 THR
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   18 ILE
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 13 optimal weight:    0.3980
   chunk 4 optimal weight:    0.0040
   chunk 17 optimal weight:    0.0050
   chunk 2 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 40 optimal weight:    0.2980
   chunk 34 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.2606

-------------------------------------------------------------------------------
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
A  78 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.131414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.120120 restraints weight = 5196.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.34
r_work: 0.3503 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3349 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.3432

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= 0.145
  Angle     :  0.678  12.360   4631  Z= 0.315
  Chirality :  0.044   0.177    516
  Planarity :  0.005   0.057    590
  Dihedral  :  4.854  30.324    470
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.72 %
    Favored  : 90.28 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 24.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.91 (0.41), residues: 422
  helix: -5.01 (0.32), residues: 12
  sheet: -0.26 (0.43), residues: 139
  loop : -1.72 (0.39), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  63 
 TYR   0.016   0.001   TYR C 421 
 PHE   0.013   0.001   PHE C 400 
 TRP   0.013   0.001   TRP C 436 
 HIS   0.001   0.000   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 3389)
  covalent geometry    : angle       0.67714 ( 4619)
  SS BOND              : bond        0.00222 (    6)
  SS BOND              : angle       0.86453 (   12)
  hydrogen bonds       : bond        0.03134 (   77)
  hydrogen bonds       : angle       5.87219 (  177)

********************** 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
  103 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
REVERT: C  357 ARG cc_start: 0.7986 (ptp-110) cc_final: 0.7772 (ptp-110)
REVERT: C  408 ARG cc_start: 0.8681 (ptm160) cc_final: 0.8413 (ptm160)
REVERT: C  414 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7725 (mm-40)
REVERT: C  429 PHE cc_start: 0.8143 (t80) cc_final: 0.7832 (t80)
REVERT: C  438 SER cc_start: 0.8655 (p) cc_final: 0.8357 (p)
REVERT: C  445 VAL cc_start: 0.8694 (t) cc_final: 0.8481 (m)
REVERT: C  473 TYR cc_start: 0.6770 (t80) cc_final: 0.6422 (t80)
REVERT: C  523 THR cc_start: 0.8045 (p) cc_final: 0.7676 (t)
REVERT: A   20 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8241 (mt)
REVERT: A   87 MET cc_start: 0.6416 (mmm) cc_final: 0.5660 (mmm)
REVERT: A   92 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8649 (p)
REVERT: B   18 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7958 (pt)
REVERT: B   55 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.6982 (mptp)
REVERT: B   78 SER cc_start: 0.7729 (t) cc_final: 0.7288 (p)
REVERT: B   83 GLU cc_start: 0.8071 (mp0) cc_final: 0.7461 (mp0)
  outliers start: 11
  outliers final: 7
  residues processed: 99
  average time/residue: 0.2603
  time to fit residues: 27.2823
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  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  430 THR
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   68 SER
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue   18 ILE
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 22 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0770
   chunk 38 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0970
   chunk 23 optimal weight:    0.0570
   chunk 27 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 9 optimal weight:    0.4980
   chunk 13 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.2654

-------------------------------------------------------------------------------
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 = 0.3798 r_free = 0.3798 target = 0.133634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.122358 restraints weight = 5277.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 2.35
r_work: 0.3508 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   3395  Z= 0.148
  Angle     :  0.687  12.753   4631  Z= 0.316
  Chirality :  0.043   0.140    516
  Planarity :  0.005   0.058    590
  Dihedral  :  4.841  29.681    470
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.48 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 24.86 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.41), residues: 422
  helix: -4.99 (0.33), residues: 12
  sheet: -0.32 (0.43), residues: 142
  loop : -1.68 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 408 
 TYR   0.016   0.001   TYR C 421 
 PHE   0.014   0.002   PHE A  24 
 TRP   0.013   0.001   TRP C 436 
 HIS   0.001   0.000   HIS B  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 3389)
  covalent geometry    : angle       0.68617 ( 4619)
  SS BOND              : bond        0.00224 (    6)
  SS BOND              : angle       0.95105 (   12)
  hydrogen bonds       : bond        0.03093 (   77)
  hydrogen bonds       : angle       5.80691 (  177)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1490.16 seconds
wall clock time: 26 minutes 2.97 seconds (1562.97 seconds total)