Starting phenix.real_space_refine
on Tue Mar  3 11:31:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wtg_32785/03_2026/7wtg_32785.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wtg_32785/03_2026/7wtg_32785.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wtg_32785/03_2026/7wtg_32785.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wtg_32785/03_2026/7wtg_32785.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wtg_32785/03_2026/7wtg_32785.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wtg_32785/03_2026/7wtg_32785.map"
  }
  resolution = 3.8
  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=   0.001
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      17      5.16       5
     C    2107      2.51       5
     N     563      2.21       5
     O     631      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 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: 3318
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "E"
      Number of atoms: 1612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1612
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 12, 'TRANS': 188}
    Chain: "H"
      Number of atoms: 918
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 918
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "L"
      Number of atoms: 788
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 788
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 6, 'TRANS': 97}
  Time building chain proxies: 0.92, per 1000 atoms: 0.28
  Number of scatterers: 3318
  At special positions: 0
  Unit cell: (60.32, 64.48, 115.44, 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      17     16.00
     O     631      8.00
     N     563      7.00
     C    2107      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.02
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " 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: 0.24
  Conformation dependent library (CDL) restraints added in 152.0 milliseconds
  

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  778

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 8 sheets defined
      5.2% alpha, 22.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'E' and resid 337 through 343
      removed outlier: 3.596A  pdb=" N   VAL E 341 " --> pdb=" O   PRO E 337 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 370
    Processing helix  chain 'E' and resid 403 through 405
      No H-bonds generated for 'chain 'E' and resid 403 through 405'
    Processing helix  chain 'E' and resid 406 through 411
      removed outlier: 3.762A  pdb=" N   ILE E 410 " --> pdb=" O   GLU E 406 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   ALA E 411 " --> pdb=" O   VAL E 407 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 406 through 411'
    Processing sheet with id=AA1, first strand: chain 'E' and resid 356 through 358
      removed outlier: 4.408A  pdb=" N   ASN E 394 " --> pdb=" O   GLU E 516 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   GLU E 516 " --> pdb=" O   ASN E 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'E' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA5, first strand: chain 'H' and resid 58 through 60
      removed outlier: 3.513A  pdb=" N   ASN H  59 " --> pdb=" O   GLY H  50 " (cutoff:3.500A)
      removed outlier: 5.656A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 8.010A  pdb=" N   ALA H  33 " --> pdb=" O   LEU H  99 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   LEU H  99 " --> pdb=" O   ALA H  33 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 6
    Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 48
      removed outlier: 7.248A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 45 through 48
      removed outlier: 7.248A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    74 hydrogen bonds defined for protein.
    180 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: 0.44

  Time building geometry restraints manager: 0.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1064
        1.35 -     1.47: 930
        1.47 -     1.60: 1389
        1.60 -     1.73: 0
        1.73 -     1.85: 21
  Bond restraints: 3404
  Sorted by residual:
  bond pdb=" N   VAL E 445 "
       pdb=" CA  VAL E 445 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.19e-02 7.06e+03 8.77e+00
  bond pdb=" N   LYS E 444 "
       pdb=" CA  LYS E 444 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.032 1.21e-02 6.83e+03 7.14e+00
  bond pdb=" N   GLY E 447 "
       pdb=" CA  GLY E 447 "
    ideal  model  delta    sigma   weight residual
    1.450  1.476 -0.025 1.01e-02 9.80e+03 6.18e+00
  bond pdb=" N   SER E 446 "
       pdb=" CA  SER E 446 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.21e-02 6.83e+03 4.66e+00
  bond pdb=" CA  VAL L  58 "
       pdb=" CB  VAL L  58 "
    ideal  model  delta    sigma   weight residual
    1.537  1.563 -0.026 1.29e-02 6.01e+03 4.06e+00
  ... (remaining 3399 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 4350
        2.34 -     4.68: 212
        4.68 -     7.03: 43
        7.03 -     9.37: 13
        9.37 -    11.71: 2
  Bond angle restraints: 4620
  Sorted by residual:
  angle pdb=" C   ILE E 410 "
        pdb=" N   ALA E 411 "
        pdb=" CA  ALA E 411 "
      ideal   model   delta    sigma   weight residual
     120.60  127.40   -6.80 1.53e+00 4.27e-01 1.98e+01
  angle pdb=" C   GLY H 113 "
        pdb=" N   MET H 114 "
        pdb=" CA  MET H 114 "
      ideal   model   delta    sigma   weight residual
     121.54  129.65   -8.11 1.91e+00 2.74e-01 1.80e+01
  angle pdb=" N   TYR L  94 "
        pdb=" CA  TYR L  94 "
        pdb=" C   TYR L  94 "
      ideal   model   delta    sigma   weight residual
     109.81  119.12   -9.31 2.21e+00 2.05e-01 1.77e+01
  angle pdb=" CA  GLY E 447 "
        pdb=" C   GLY E 447 "
        pdb=" O   GLY E 447 "
      ideal   model   delta    sigma   weight residual
     122.05  118.00    4.05 1.00e+00 1.00e+00 1.64e+01
  angle pdb=" C   GLN H  62 "
        pdb=" N   LYS H  63 "
        pdb=" CA  LYS H  63 "
      ideal   model   delta    sigma   weight residual
     121.54  128.80   -7.26 1.91e+00 2.74e-01 1.44e+01
  ... (remaining 4615 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 1798
       17.95 -    35.90: 181
       35.90 -    53.84: 29
       53.84 -    71.79: 4
       71.79 -    89.74: 5
  Dihedral angle restraints: 2017
    sinusoidal: 790
      harmonic: 1227
  Sorted by residual:
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.13  -72.13     1      1.00e+01 1.00e-02 6.65e+01
  dihedral pdb=" CA  CYS E 361 "
           pdb=" C   CYS E 361 "
           pdb=" N   VAL E 362 "
           pdb=" CA  VAL E 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.00   39.00     0      5.00e+00 4.00e-02 6.08e+01
  dihedral pdb=" CA  PRO E 337 "
           pdb=" C   PRO E 337 "
           pdb=" N   PHE E 338 "
           pdb=" CA  PHE E 338 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.52   30.48     0      5.00e+00 4.00e-02 3.72e+01
  ... (remaining 2014 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 349
       0.058 -    0.116: 95
       0.116 -    0.174: 34
       0.174 -    0.233: 8
       0.233 -    0.291: 4
  Chirality restraints: 490
  Sorted by residual:
  chirality pdb=" CB  THR L  85 "
            pdb=" CA  THR L  85 "
            pdb=" OG1 THR L  85 "
            pdb=" CG2 THR L  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.26    0.29 2.00e-01 2.50e+01 2.11e+00
  chirality pdb=" CB  VAL L  58 "
            pdb=" CA  VAL L  58 "
            pdb=" CG1 VAL L  58 "
            pdb=" CG2 VAL L  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" CA  ASN E 354 "
            pdb=" N   ASN E 354 "
            pdb=" C   ASN E 354 "
            pdb=" CB  ASN E 354 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.98e+00
  ... (remaining 487 not shown)

  Planarity restraints: 601
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 462 "    0.053 5.00e-02 4.00e+02   8.00e-02 1.02e+01
        pdb=" N   PRO E 463 "   -0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO E 463 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO E 463 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 453 "    0.022 2.00e-02 2.50e+03   2.12e-02 9.01e+00
        pdb=" CG  TYR E 453 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 453 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 453 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 453 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 453 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 453 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR E 453 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL L  58 "    0.049 5.00e-02 4.00e+02   7.48e-02 8.96e+00
        pdb=" N   PRO L  59 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO L  59 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO L  59 "    0.041 5.00e-02 4.00e+02
  ... (remaining 598 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 922
        2.82 -     3.34: 2655
        3.34 -     3.86: 5232
        3.86 -     4.38: 5684
        4.38 -     4.90: 10127
  Nonbonded interactions: 24620
  Sorted by model distance:
  nonbonded pdb=" O   SER L  60 "
            pdb=" OG  SER L  60 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   ILE L   2 "
            pdb=" OG1 THR L  97 "
     model   vdw
     2.349 3.040
  nonbonded pdb=" NH2 ARG H  67 "
            pdb=" OD2 ASP H  90 "
     model   vdw
     2.364 3.120
  nonbonded pdb=" OD2 ASP E 398 "
            pdb=" OH  TYR E 423 "
     model   vdw
     2.396 3.040
  nonbonded pdb=" OG1 THR L  85 "
            pdb=" O   GLY L 101 "
     model   vdw
     2.398 3.040
  ... (remaining 24615 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.010
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.940
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
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      :  0.006   0.050   3410  Z= 0.294
  Angle     :  1.208  11.712   4632  Z= 0.647
  Chirality :  0.069   0.291    490
  Planarity :  0.011   0.083    601
  Dihedral  : 14.445  89.737   1221
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.50 %

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: -2.94 (0.36), residues: 419
  helix: -4.41 (0.43), residues: 30
  sheet: -0.69 (0.47), residues: 125
  loop : -2.41 (0.32), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.002   ARG H 108 
 TYR   0.050   0.003   TYR E 453 
 PHE   0.035   0.004   PHE E 377 
 TRP   0.039   0.004   TRP H 117 
 HIS   0.002   0.001   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00589 ( 3404)
  covalent geometry    : angle       1.20107 ( 4620)
  SS BOND              : bond        0.01021 (    6)
  SS BOND              : angle       2.82842 (   12)
  hydrogen bonds       : bond        0.14264 (   65)
  hydrogen bonds       : angle       9.09702 (  180)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  386 LYS cc_start: 0.8112 (pttt) cc_final: 0.7753 (tptm)
REVERT: L   27 GLN cc_start: 0.7584 (tm-30) cc_final: 0.7296 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.0775
  time to fit residues: 8.1485
Evaluate side-chains
  76 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.0470
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
L  90 GLN
L  92 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.174516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.147786 restraints weight = 4341.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.146685 restraints weight = 4180.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.148143 restraints weight = 3930.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.148461 restraints weight = 3038.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.148839 restraints weight = 2767.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3410  Z= 0.191
  Angle     :  0.700   7.970   4632  Z= 0.366
  Chirality :  0.047   0.213    490
  Planarity :  0.006   0.062    601
  Dihedral  :  6.091  35.850    470
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.88 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 12.78 %
    Favored  : 85.28 %
  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 (0.37), residues: 419
  helix: -3.55 (0.74), residues: 30
  sheet: -0.57 (0.48), residues: 119
  loop : -2.38 (0.32), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H 108 
 TYR   0.020   0.002   TYR E 453 
 PHE   0.020   0.002   PHE H  64 
 TRP   0.015   0.002   TRP H  36 
 HIS   0.003   0.001   HIS E 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 3404)
  covalent geometry    : angle       0.69508 ( 4620)
  SS BOND              : bond        0.00611 (    6)
  SS BOND              : angle       1.81152 (   12)
  hydrogen bonds       : bond        0.03295 (   65)
  hydrogen bonds       : angle       6.44045 (  180)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 6
  residues processed: 88
  average time/residue: 0.0813
  time to fit residues: 8.4026
Evaluate side-chains
  75 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  432 CYS
Chi-restraints excluded: chain E residue  512 VAL
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue   77 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0040
   chunk 17 optimal weight:    0.2980
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0270
   chunk 22 optimal weight:    3.9990
   chunk 26 optimal weight:    0.1980
   chunk 20 optimal weight:    0.8980
   chunk 1 optimal weight:    0.3980
   overall best weight:    0.1850

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

Flipped N/Q/H residues before XYZ refinement:
E 343 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.172961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.146411 restraints weight = 4271.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.146186 restraints weight = 3589.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.147794 restraints weight = 3405.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.148284 restraints weight = 2634.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.148739 restraints weight = 2373.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.2582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3410  Z= 0.114
  Angle     :  0.615   7.208   4632  Z= 0.316
  Chirality :  0.045   0.176    490
  Planarity :  0.005   0.052    601
  Dihedral  :  5.430  32.184    470
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 18.89 %
    Favored  : 79.72 %
  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: -2.36 (0.38), residues: 419
  helix: -2.55 (1.01), residues: 24
  sheet: -0.46 (0.48), residues: 117
  loop : -2.10 (0.33), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H 108 
 TYR   0.011   0.001   TYR L  49 
 PHE   0.023   0.001   PHE E 456 
 TRP   0.018   0.001   TRP H  36 
 HIS   0.001   0.000   HIS E 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 3404)
  covalent geometry    : angle       0.61126 ( 4620)
  SS BOND              : bond        0.00462 (    6)
  SS BOND              : angle       1.42723 (   12)
  hydrogen bonds       : bond        0.02964 (   65)
  hydrogen bonds       : angle       5.67984 (  180)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  498 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.7795 (mtm-85)
REVERT: H  110 TYR cc_start: 0.7401 (t80) cc_final: 0.7137 (t80)
  outliers start: 5
  outliers final: 5
  residues processed: 77
  average time/residue: 0.0962
  time to fit residues: 8.5355
Evaluate side-chains
  77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  432 CYS
Chi-restraints excluded: chain H residue   48 MET
Chi-restraints excluded: chain H residue   52 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue    2 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 18 optimal weight:    0.4980
   chunk 24 optimal weight:    0.2980
   chunk 8 optimal weight:    0.6980
   chunk 2 optimal weight:    0.3980
   chunk 12 optimal weight:    0.0770
   chunk 39 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.3738

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

Flipped N/Q/H residues before XYZ refinement:
E 343 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.167870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.140446 restraints weight = 4204.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.141524 restraints weight = 3555.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.143200 restraints weight = 3418.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.143450 restraints weight = 2236.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.143831 restraints weight = 2108.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3410  Z= 0.160
  Angle     :  0.642   7.671   4632  Z= 0.331
  Chirality :  0.046   0.201    490
  Planarity :  0.005   0.051    601
  Dihedral  :  5.521  32.664    470
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 20.56 %
    Favored  : 76.67 %
  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: -2.25 (0.38), residues: 419
  helix: -1.97 (1.13), residues: 24
  sheet: -0.62 (0.47), residues: 118
  loop : -1.95 (0.33), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  61 
 TYR   0.016   0.002   TYR L  49 
 PHE   0.019   0.002   PHE H  64 
 TRP   0.020   0.002   TRP H  36 
 HIS   0.001   0.000   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 3404)
  covalent geometry    : angle       0.63701 ( 4620)
  SS BOND              : bond        0.00550 (    6)
  SS BOND              : angle       1.71421 (   12)
  hydrogen bonds       : bond        0.02905 (   65)
  hydrogen bonds       : angle       5.48446 (  180)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
REVERT: H   19 LYS cc_start: 0.7412 (tppp) cc_final: 0.7053 (tptt)
REVERT: H  110 TYR cc_start: 0.7780 (t80) cc_final: 0.7540 (t80)
  outliers start: 10
  outliers final: 6
  residues processed: 79
  average time/residue: 0.0955
  time to fit residues: 8.7187
Evaluate side-chains
  75 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  512 VAL
Chi-restraints excluded: chain H residue   48 MET
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue    5 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0170
   chunk 25 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 1 optimal weight:    0.1980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.4418

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

Flipped N/Q/H residues before XYZ refinement:
E 343 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.166219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.139041 restraints weight = 4325.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.139072 restraints weight = 3778.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.141267 restraints weight = 3430.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.141364 restraints weight = 2382.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.141685 restraints weight = 2260.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3410  Z= 0.178
  Angle     :  0.664   8.279   4632  Z= 0.343
  Chirality :  0.046   0.211    490
  Planarity :  0.005   0.050    601
  Dihedral  :  5.658  33.113    470
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.55 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 21.67 %
    Favored  : 76.11 %
  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: -2.25 (0.38), residues: 419
  helix: -2.08 (1.06), residues: 24
  sheet: -0.60 (0.47), residues: 119
  loop : -1.96 (0.33), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E 498 
 TYR   0.016   0.002   TYR E 453 
 PHE   0.021   0.002   PHE H  64 
 TRP   0.025   0.003   TRP H  36 
 HIS   0.001   0.000   HIS E 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 3404)
  covalent geometry    : angle       0.65753 ( 4620)
  SS BOND              : bond        0.00624 (    6)
  SS BOND              : angle       1.97591 (   12)
  hydrogen bonds       : bond        0.02867 (   65)
  hydrogen bonds       : angle       5.32064 (  180)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  400 PHE cc_start: 0.8883 (m-80) cc_final: 0.8593 (m-80)
REVERT: H   19 LYS cc_start: 0.7469 (tppp) cc_final: 0.7172 (tptt)
  outliers start: 8
  outliers final: 6
  residues processed: 80
  average time/residue: 0.0884
  time to fit residues: 8.2690
Evaluate side-chains
  81 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  512 VAL
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   48 MET
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue    2 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 1 optimal weight:    0.1980
   chunk 35 optimal weight:    0.0980
   chunk 23 optimal weight:    0.3980
   chunk 28 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0980
   chunk 3 optimal weight:    0.0970
   chunk 37 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.1778

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

Flipped N/Q/H residues before XYZ refinement:
E 477 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.170025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.143461 restraints weight = 4220.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.144175 restraints weight = 3432.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.145601 restraints weight = 2997.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.145951 restraints weight = 2371.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.146411 restraints weight = 2145.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.3298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3410  Z= 0.113
  Angle     :  0.621   7.728   4632  Z= 0.317
  Chirality :  0.044   0.167    490
  Planarity :  0.005   0.052    601
  Dihedral  :  5.197  29.900    470
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.88 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 20.56 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.03 (0.39), residues: 419
  helix: -1.86 (1.11), residues: 24
  sheet: -0.45 (0.48), residues: 119
  loop : -1.81 (0.34), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  61 
 TYR   0.008   0.001   TYR E 423 
 PHE   0.021   0.001   PHE E 456 
 TRP   0.014   0.001   TRP H  36 
 HIS   0.001   0.000   HIS E 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 3404)
  covalent geometry    : angle       0.61712 ( 4620)
  SS BOND              : bond        0.00492 (    6)
  SS BOND              : angle       1.54004 (   12)
  hydrogen bonds       : bond        0.02646 (   65)
  hydrogen bonds       : angle       4.92723 (  180)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 LYS cc_start: 0.7418 (tppp) cc_final: 0.7142 (tptt)
  outliers start: 16
  outliers final: 7
  residues processed: 87
  average time/residue: 0.0799
  time to fit residues: 8.1650
Evaluate side-chains
  81 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  512 VAL
Chi-restraints excluded: chain H residue   48 MET
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   67 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 0 optimal weight:    0.8980
   chunk 13 optimal weight:    0.2980
   chunk 3 optimal weight:    0.0980
   chunk 30 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 22 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 17 optimal weight:    0.4980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
E 343 ASN
E 477 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.165091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.137742 restraints weight = 4355.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.137079 restraints weight = 3889.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.138429 restraints weight = 3517.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.139164 restraints weight = 2688.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.139789 restraints weight = 2430.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.3590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3410  Z= 0.184
  Angle     :  0.680   8.256   4632  Z= 0.350
  Chirality :  0.047   0.211    490
  Planarity :  0.005   0.053    601
  Dihedral  :  5.569  32.658    470
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.79 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 22.22 %
    Favored  : 74.17 %
  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: -2.20 (0.38), residues: 419
  helix: -2.39 (1.15), residues: 18
  sheet: -0.58 (0.48), residues: 119
  loop : -1.90 (0.33), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  61 
 TYR   0.017   0.002   TYR L  49 
 PHE   0.027   0.002   PHE E 456 
 TRP   0.028   0.002   TRP H  36 
 HIS   0.002   0.001   HIS E 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 3404)
  covalent geometry    : angle       0.67420 ( 4620)
  SS BOND              : bond        0.00654 (    6)
  SS BOND              : angle       1.83711 (   12)
  hydrogen bonds       : bond        0.02831 (   65)
  hydrogen bonds       : angle       5.14264 (  180)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
REVERT: E  400 PHE cc_start: 0.8899 (m-80) cc_final: 0.8650 (m-80)
REVERT: E  467 ASP cc_start: 0.7764 (p0) cc_final: 0.7543 (p0)
REVERT: H   19 LYS cc_start: 0.7486 (tppp) cc_final: 0.7203 (tptt)
  outliers start: 13
  outliers final: 9
  residues processed: 80
  average time/residue: 0.0797
  time to fit residues: 7.4992
Evaluate side-chains
  74 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  512 VAL
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   48 MET
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   77 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 37 optimal weight:    0.0670
   chunk 33 optimal weight:    3.9990
   chunk 6 optimal weight:    0.3980
   chunk 3 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0170
   chunk 27 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.3956

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

Flipped N/Q/H residues before XYZ refinement:
E 343 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.163776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.136361 restraints weight = 4365.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.135387 restraints weight = 4001.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.137469 restraints weight = 3898.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.137914 restraints weight = 2783.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.138210 restraints weight = 2421.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3410  Z= 0.168
  Angle     :  0.675   8.136   4632  Z= 0.349
  Chirality :  0.047   0.206    490
  Planarity :  0.006   0.054    601
  Dihedral  :  5.517  32.251    470
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 23.06 %
    Favored  : 73.06 %
  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: -2.23 (0.38), residues: 419
  helix: -2.33 (1.17), residues: 18
  sheet: -0.69 (0.48), residues: 119
  loop : -1.88 (0.33), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  61 
 TYR   0.014   0.002   TYR L  49 
 PHE   0.027   0.002   PHE E 456 
 TRP   0.024   0.002   TRP H  36 
 HIS   0.001   0.000   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 3404)
  covalent geometry    : angle       0.66999 ( 4620)
  SS BOND              : bond        0.00688 (    6)
  SS BOND              : angle       1.72086 (   12)
  hydrogen bonds       : bond        0.02731 (   65)
  hydrogen bonds       : angle       5.05073 (  180)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: E  400 PHE cc_start: 0.8837 (m-80) cc_final: 0.8576 (m-80)
REVERT: E  467 ASP cc_start: 0.7731 (p0) cc_final: 0.7433 (p0)
REVERT: H   19 LYS cc_start: 0.7465 (tppp) cc_final: 0.7190 (tptt)
  outliers start: 14
  outliers final: 11
  residues processed: 82
  average time/residue: 0.0790
  time to fit residues: 7.7002
Evaluate side-chains
  82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  480 CYS
Chi-restraints excluded: chain E residue  512 VAL
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   48 MET
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   81 MET
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   77 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
E 343 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.159562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.131604 restraints weight = 4398.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.130952 restraints weight = 3807.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.132132 restraints weight = 3449.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.133303 restraints weight = 2698.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.133516 restraints weight = 2380.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.4315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052   3410  Z= 0.282
  Angle     :  0.790   9.992   4632  Z= 0.414
  Chirality :  0.051   0.276    490
  Planarity :  0.006   0.051    601
  Dihedral  :  6.323  36.910    470
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.17 %
    Favored  : 87.83 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 22.78 %
    Favored  : 73.33 %
  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: -2.74 (0.37), residues: 419
  helix: -2.95 (1.07), residues: 18
  sheet: -0.96 (0.47), residues: 119
  loop : -2.27 (0.32), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  61 
 TYR   0.020   0.002   TYR E 453 
 PHE   0.031   0.003   PHE H  64 
 TRP   0.028   0.003   TRP H  36 
 HIS   0.001   0.000   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00659 ( 3404)
  covalent geometry    : angle       0.78110 ( 4620)
  SS BOND              : bond        0.00963 (    6)
  SS BOND              : angle       2.43102 (   12)
  hydrogen bonds       : bond        0.03200 (   65)
  hydrogen bonds       : angle       5.46587 (  180)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  378 LYS cc_start: 0.8421 (tptp) cc_final: 0.7973 (tppt)
REVERT: E  467 ASP cc_start: 0.7902 (p0) cc_final: 0.7623 (p0)
REVERT: E  492 LEU cc_start: 0.8564 (mp) cc_final: 0.8172 (mp)
  outliers start: 14
  outliers final: 11
  residues processed: 86
  average time/residue: 0.0796
  time to fit residues: 8.1115
Evaluate side-chains
  88 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  480 CYS
Chi-restraints excluded: chain E residue  512 VAL
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue   48 MET
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   77 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0270
   chunk 17 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
E 343 ASN
** L  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.159824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.133525 restraints weight = 4304.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.133723 restraints weight = 3860.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.135011 restraints weight = 3821.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.135665 restraints weight = 2722.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.136679 restraints weight = 2495.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.4424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   3410  Z= 0.220
  Angle     :  0.827  12.055   4632  Z= 0.428
  Chirality :  0.051   0.242    490
  Planarity :  0.006   0.054    601
  Dihedral  :  6.163  35.656    470
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  : 10.02 %
    Favored  : 89.74 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 24.44 %
    Favored  : 72.50 %
  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: -2.85 (0.36), residues: 419
  helix: -3.42 (0.82), residues: 24
  sheet: -0.93 (0.47), residues: 119
  loop : -2.33 (0.31), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  61 
 TYR   0.017   0.002   TYR L  49 
 PHE   0.027   0.003   PHE E 456 
 TRP   0.026   0.003   TRP H  36 
 HIS   0.001   0.000   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 ( 3404)
  covalent geometry    : angle       0.80444 ( 4620)
  SS BOND              : bond        0.00822 (    6)
  SS BOND              : angle       3.83192 (   12)
  hydrogen bonds       : bond        0.03194 (   65)
  hydrogen bonds       : angle       5.29760 (  180)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  378 LYS cc_start: 0.8331 (tptp) cc_final: 0.7981 (tppt)
REVERT: E  467 ASP cc_start: 0.7655 (p0) cc_final: 0.7354 (p0)
  outliers start: 11
  outliers final: 10
  residues processed: 83
  average time/residue: 0.0861
  time to fit residues: 8.3671
Evaluate side-chains
  85 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  480 CYS
Chi-restraints excluded: chain E residue  512 VAL
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue   48 MET
Chi-restraints excluded: chain H residue   54 ILE
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   67 SER
Chi-restraints excluded: chain L residue   77 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 2 optimal weight:    0.3980
   chunk 24 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
E 343 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.157654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.131294 restraints weight = 4423.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.132484 restraints weight = 3935.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.133795 restraints weight = 3504.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.133861 restraints weight = 2545.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.134481 restraints weight = 2307.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.4587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   3410  Z= 0.234
  Angle     :  0.808   9.044   4632  Z= 0.420
  Chirality :  0.050   0.244    490
  Planarity :  0.006   0.052    601
  Dihedral  :  6.287  35.947    470
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  : 10.98 %
    Favored  : 88.78 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 24.17 %
    Favored  : 73.06 %
  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: -2.94 (0.36), residues: 419
  helix: -3.46 (0.82), residues: 24
  sheet: -0.96 (0.48), residues: 118
  loop : -2.41 (0.31), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  61 
 TYR   0.018   0.002   TYR L  49 
 PHE   0.028   0.003   PHE E 456 
 TRP   0.028   0.003   TRP H  36 
 HIS   0.001   0.001   HIS H 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00550 ( 3404)
  covalent geometry    : angle       0.78744 ( 4620)
  SS BOND              : bond        0.00790 (    6)
  SS BOND              : angle       3.64359 (   12)
  hydrogen bonds       : bond        0.03138 (   65)
  hydrogen bonds       : angle       5.39299 (  180)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 857.12 seconds
wall clock time: 15 minutes 23.65 seconds (923.65 seconds total)