Starting phenix.real_space_refine
on Tue Mar  3 12:55:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dad_27270/03_2026/8dad_27270.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dad_27270/03_2026/8dad_27270.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dad_27270/03_2026/8dad_27270.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dad_27270/03_2026/8dad_27270.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dad_27270/03_2026/8dad_27270.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dad_27270/03_2026/8dad_27270.map"
  }
  resolution = 3.85
  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=  -0.001 sd=   0.044
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1656 atoms to isotropic.
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      19      5.16       5
     C    2068      2.51       5
     N     558      2.21       5
     O     610      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 3255
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "H"
      Number of atoms: 955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 955
          Classifications: {'peptide': 123}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 3, 'TRANS': 119}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "L"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 816
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 1428
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1428
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 42}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 139
          Unresolved non-hydrogen dihedrals: 86
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 5, 'GLN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 55
    Chain: "J"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 0.97, per 1000 atoms: 0.30
  Number of scatterers: 3255
  At special positions: 0
  Unit cell: (62.83, 64.89, 101.97, 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      19     16.00
     O     610      8.00
     N     558      7.00
     C    2068      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 101 " - pdb=" SG  CYS H 106 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " 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
  Links applied
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG J   1 " - " NAG J   2 "
    NAG-ASN
      " NAG A   1 " - " ASN B 343 "
  Time building additional restraints: 0.30
  Conformation dependent library (CDL) restraints added in 83.4 milliseconds
  

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  780

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 8 sheets defined
      12.0% alpha, 32.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'L' and resid 30 through 32
      No H-bonds generated for 'chain 'L' and resid 30 through 32'
    Processing helix  chain 'L' and resid 80 through 84
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 349 through 353
    Processing helix  chain 'B' and resid 364 through 371
      removed outlier: 3.898A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.194A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.215A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.546A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.585A  pdb=" N   MET H 112 " --> pdb=" O   ALA H  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.638A  pdb=" N   LEU L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   TYR L  50 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358
    Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474

    121 hydrogen bonds defined for protein.
    285 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: 0.59

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1052
        1.34 -     1.46: 889
        1.46 -     1.58: 1371
        1.58 -     1.70: 0
        1.70 -     1.83: 24
  Bond restraints: 3336
  Sorted by residual:
  bond pdb=" C1  NAG J   2 "
       pdb=" O5  NAG J   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.21e+00
  bond pdb=" C1  NAG A   1 "
       pdb=" O5  NAG A   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.19e+00
  bond pdb=" C1  NAG A   2 "
       pdb=" O5  NAG A   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.94e+00
  bond pdb=" C1  NAG J   1 "
       pdb=" C2  NAG J   1 "
    ideal  model  delta    sigma   weight residual
    1.532  1.506  0.026 2.00e-02 2.50e+03 1.76e+00
  bond pdb=" C5  NAG J   1 "
       pdb=" O5  NAG J   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.439 -0.026 2.00e-02 2.50e+03 1.72e+00
  ... (remaining 3331 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.54: 4452
        2.54 -     5.09: 78
        5.09 -     7.63: 11
        7.63 -    10.17: 1
       10.17 -    12.72: 2
  Bond angle restraints: 4544
  Sorted by residual:
  angle pdb=" N   CYS B 391 "
        pdb=" CA  CYS B 391 "
        pdb=" C   CYS B 391 "
      ideal   model   delta    sigma   weight residual
     107.69  120.41  -12.72 2.01e+00 2.48e-01 4.00e+01
  angle pdb=" N   LEU B 390 "
        pdb=" CA  LEU B 390 "
        pdb=" C   LEU B 390 "
      ideal   model   delta    sigma   weight residual
     109.76  115.86   -6.10 1.59e+00 3.96e-01 1.47e+01
  angle pdb=" CA  CYS B 391 "
        pdb=" CB  CYS B 391 "
        pdb=" SG  CYS B 391 "
      ideal   model   delta    sigma   weight residual
     114.40  122.98   -8.58 2.30e+00 1.89e-01 1.39e+01
  angle pdb=" CB  MET H 118 "
        pdb=" CG  MET H 118 "
        pdb=" SD  MET H 118 "
      ideal   model   delta    sigma   weight residual
     112.70  123.10  -10.40 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" CA  CYS B 525 "
        pdb=" CB  CYS B 525 "
        pdb=" SG  CYS B 525 "
      ideal   model   delta    sigma   weight residual
     114.40  121.52   -7.12 2.30e+00 1.89e-01 9.57e+00
  ... (remaining 4539 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.03: 1767
       20.03 -    40.07: 195
       40.07 -    60.10: 38
       60.10 -    80.13: 7
       80.13 -   100.17: 10
  Dihedral angle restraints: 2017
    sinusoidal: 791
      harmonic: 1226
  Sorted by residual:
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -166.15   80.15     1      1.00e+01 1.00e-02 7.96e+01
  dihedral pdb=" CB  CYS B 391 "
           pdb=" SG  CYS B 391 "
           pdb=" SG  CYS B 525 "
           pdb=" CB  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   19.42   73.58     1      1.00e+01 1.00e-02 6.89e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  89 "
           pdb=" CB  CYS L  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  164.39  -71.39     1      1.00e+01 1.00e-02 6.54e+01
  ... (remaining 2014 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 477
       0.106 -    0.212: 23
       0.212 -    0.318: 0
       0.318 -    0.424: 0
       0.424 -    0.529: 1
  Chirality restraints: 501
  Sorted by residual:
  chirality pdb=" CA  CYS B 391 "
            pdb=" N   CYS B 391 "
            pdb=" C   CYS B 391 "
            pdb=" CB  CYS B 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.53 2.00e-01 2.50e+01 7.00e+00
  chirality pdb=" C4  NAG J   1 "
            pdb=" C3  NAG J   1 "
            pdb=" C5  NAG J   1 "
            pdb=" O4  NAG J   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.34   -0.19 2.00e-01 2.50e+01 8.72e-01
  chirality pdb=" C1  NAG A   2 "
            pdb=" O4  NAG A   1 "
            pdb=" C2  NAG A   2 "
            pdb=" O5  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.38   -0.02 2.00e-02 2.50e+03 7.44e-01
  ... (remaining 498 not shown)

  Planarity restraints: 589
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP L  36 "   -0.012 2.00e-02 2.50e+03   1.85e-02 8.60e+00
        pdb=" CG  TRP L  36 "    0.049 2.00e-02 2.50e+03
        pdb=" CD1 TRP L  36 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP L  36 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP L  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP L  36 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP L  36 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ2 TRP L  36 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP L  36 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP L  36 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY H   8 "   -0.035 5.00e-02 4.00e+02   5.36e-02 4.61e+00
        pdb=" N   PRO H   9 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO H   9 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO H   9 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 526 "   -0.028 5.00e-02 4.00e+02   4.28e-02 2.93e+00
        pdb=" N   PRO B 527 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 527 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 527 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 586 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 631
        2.77 -     3.30: 3114
        3.30 -     3.84: 5612
        3.84 -     4.37: 6247
        4.37 -     4.90: 10905
  Nonbonded interactions: 26509
  Sorted by model distance:
  nonbonded pdb=" N   GLU H  66 "
            pdb=" OE1 GLU H  66 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" OH  TYR L  37 "
            pdb=" OE1 GLN L  90 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   THR H 104 "
            pdb=" OH  TYR B 473 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" OD2 ASP H 108 "
            pdb=" NH1 ARG L  54 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" N   GLN H  65 "
            pdb=" OE1 GLN H  65 "
     model   vdw
     2.317 3.120
  ... (remaining 26504 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'J'
}

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:             3.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.300
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
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      :  0.004   0.033   3346  Z= 0.201
  Angle     :  0.846  12.716   4567  Z= 0.434
  Chirality :  0.054   0.529    501
  Planarity :  0.006   0.054    588
  Dihedral  : 17.766 100.167   1216
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 16.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 26.98 %
    Favored  : 72.38 %
  Cbeta Deviations :  0.26 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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: -0.96 (0.42), residues: 418
  helix: -2.01 (0.96), residues: 33
  sheet: -0.55 (0.44), residues: 146
  loop : -0.37 (0.41), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  38 
 TYR   0.009   0.001   TYR L  92 
 PHE   0.013   0.002   PHE H  27 
 TRP   0.049   0.003   TRP L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 3336)
  covalent geometry    : angle       0.83189 ( 4544)
  SS BOND              : bond        0.00269 (    7)
  SS BOND              : angle       2.79015 (   14)
  hydrogen bonds       : bond        0.13761 (  114)
  hydrogen bonds       : angle       8.19943 (  285)
  link_BETA1-4         : bond        0.00337 (    2)
  link_BETA1-4         : angle       0.81715 (    6)
  link_NAG-ASN         : bond        0.00118 (    1)
  link_NAG-ASN         : angle       1.84508 (    3)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  424 LYS cc_start: 0.8407 (ttpp) cc_final: 0.8126 (ttpp)
  outliers start: 2
  outliers final: 1
  residues processed: 79
  average time/residue: 0.1002
  time to fit residues: 9.1404
Evaluate side-chains
  72 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   34 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.4980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
L  43 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.112447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.093174 restraints weight = 8830.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.095858 restraints weight = 5948.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.097833 restraints weight = 4504.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.099254 restraints weight = 3680.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.099953 restraints weight = 3154.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
moved from start:          0.1059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3346  Z= 0.138
  Angle     :  0.676   7.058   4567  Z= 0.340
  Chirality :  0.046   0.138    501
  Planarity :  0.005   0.050    588
  Dihedral  : 10.942  75.755    556
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 25.40 %
    Favored  : 71.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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: -0.92 (0.42), residues: 418
  helix: -2.01 (0.97), residues: 34
  sheet: -0.72 (0.41), residues: 158
  loop : -0.14 (0.43), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 346 
 TYR   0.010   0.001   TYR L  92 
 PHE   0.030   0.002   PHE B 392 
 TRP   0.039   0.003   TRP L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3336)
  covalent geometry    : angle       0.66413 ( 4544)
  SS BOND              : bond        0.00342 (    7)
  SS BOND              : angle       1.91234 (   14)
  hydrogen bonds       : bond        0.03632 (  114)
  hydrogen bonds       : angle       6.81560 (  285)
  link_BETA1-4         : bond        0.00398 (    2)
  link_BETA1-4         : angle       2.09953 (    6)
  link_NAG-ASN         : bond        0.00114 (    1)
  link_NAG-ASN         : angle       1.43425 (    3)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 TRP cc_start: 0.7996 (t60) cc_final: 0.7619 (t60)
REVERT: H  112 MET cc_start: 0.8188 (mpp) cc_final: 0.6993 (mpp)
REVERT: L   78 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7790 (tmm160)
REVERT: L   80 GLU cc_start: 0.7353 (tt0) cc_final: 0.7045 (tt0)
  outliers start: 9
  outliers final: 4
  residues processed: 84
  average time/residue: 0.0868
  time to fit residues: 8.6394
Evaluate side-chains
  74 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   59 ILE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain B residue  392 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 13 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 29 optimal weight:    0.0570
   chunk 39 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 20 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
** L  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.113074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.094433 restraints weight = 8645.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.097026 restraints weight = 5989.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.098930 restraints weight = 4575.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.100299 restraints weight = 3741.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.101335 restraints weight = 3214.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.1393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3346  Z= 0.127
  Angle     :  0.700  10.330   4567  Z= 0.344
  Chirality :  0.046   0.160    501
  Planarity :  0.005   0.047    588
  Dihedral  :  9.873  67.545    555
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 24.76 %
    Favored  : 70.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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: -0.91 (0.42), residues: 418
  helix: -2.35 (0.88), residues: 34
  sheet: -0.71 (0.40), residues: 158
  loop : -0.06 (0.44), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 403 
 TYR   0.009   0.001   TYR L  92 
 PHE   0.025   0.002   PHE B 392 
 TRP   0.022   0.002   TRP L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 3336)
  covalent geometry    : angle       0.68187 ( 4544)
  SS BOND              : bond        0.00463 (    7)
  SS BOND              : angle       2.63276 (   14)
  hydrogen bonds       : bond        0.03328 (  114)
  hydrogen bonds       : angle       6.52701 (  285)
  link_BETA1-4         : bond        0.00323 (    2)
  link_BETA1-4         : angle       2.01738 (    6)
  link_NAG-ASN         : bond        0.00149 (    1)
  link_NAG-ASN         : angle       1.50027 (    3)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   38 ARG cc_start: 0.7735 (ttt180) cc_final: 0.6572 (ttt-90)
REVERT: H   46 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6971 (pm20)
REVERT: H   47 TRP cc_start: 0.8191 (t60) cc_final: 0.7701 (t60)
REVERT: H   80 TYR cc_start: 0.8193 (m-10) cc_final: 0.7989 (m-10)
REVERT: L   17 GLU cc_start: 0.6999 (pm20) cc_final: 0.6270 (pm20)
REVERT: L   78 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7667 (tmm160)
REVERT: L   80 GLU cc_start: 0.7181 (tt0) cc_final: 0.6916 (tt0)
  outliers start: 15
  outliers final: 8
  residues processed: 87
  average time/residue: 0.0756
  time to fit residues: 7.8310
Evaluate side-chains
  79 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   34 VAL
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue  122 SER
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   59 ILE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 37 optimal weight:    0.4980
   chunk 11 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
** L  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.109066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.089771 restraints weight = 8746.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.092321 restraints weight = 6021.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.094200 restraints weight = 4615.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.095556 restraints weight = 3807.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.096529 restraints weight = 3295.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   3346  Z= 0.252
  Angle     :  0.715   7.406   4567  Z= 0.362
  Chirality :  0.048   0.207    501
  Planarity :  0.005   0.049    588
  Dihedral  :  9.135  60.784    555
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 15.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 22.54 %
    Favored  : 71.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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: -0.98 (0.42), residues: 418
  helix: -2.24 (0.92), residues: 33
  sheet: -0.77 (0.41), residues: 154
  loop : -0.16 (0.43), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 346 
 TYR   0.014   0.001   TYR B 453 
 PHE   0.025   0.002   PHE B 392 
 TRP   0.020   0.003   TRP L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00565 ( 3336)
  covalent geometry    : angle       0.70318 ( 4544)
  SS BOND              : bond        0.00506 (    7)
  SS BOND              : angle       1.79108 (   14)
  hydrogen bonds       : bond        0.03781 (  114)
  hydrogen bonds       : angle       6.57714 (  285)
  link_BETA1-4         : bond        0.00288 (    2)
  link_BETA1-4         : angle       2.01774 (    6)
  link_NAG-ASN         : bond        0.00105 (    1)
  link_NAG-ASN         : angle       2.32068 (    3)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.074 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   38 ARG cc_start: 0.7946 (ttt180) cc_final: 0.7399 (ttt180)
REVERT: H   47 TRP cc_start: 0.8355 (t60) cc_final: 0.7737 (t60)
REVERT: H  112 MET cc_start: 0.8417 (mpp) cc_final: 0.7873 (mpp)
REVERT: L   17 GLU cc_start: 0.7424 (pm20) cc_final: 0.6553 (pm20)
REVERT: L   78 ARG cc_start: 0.8160 (ttp80) cc_final: 0.7763 (ttp80)
  outliers start: 20
  outliers final: 15
  residues processed: 82
  average time/residue: 0.0694
  time to fit residues: 6.8358
Evaluate side-chains
  82 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue   34 VAL
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   57 THR
Chi-restraints excluded: chain L residue   59 ILE
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  452 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0870
   chunk 38 optimal weight:    0.8980
   chunk 21 optimal weight:    0.3980
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
** L  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.112046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.093925 restraints weight = 8706.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.096280 restraints weight = 6101.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.098087 restraints weight = 4754.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.099321 restraints weight = 3919.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.100430 restraints weight = 3407.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3346  Z= 0.130
  Angle     :  0.695   8.481   4567  Z= 0.342
  Chirality :  0.046   0.136    501
  Planarity :  0.005   0.047    588
  Dihedral  :  8.460  54.983    555
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 23.17 %
    Favored  : 70.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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: -0.88 (0.42), residues: 418
  helix: -2.43 (0.87), residues: 33
  sheet: -0.75 (0.40), residues: 157
  loop :  0.01 (0.44), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 346 
 TYR   0.010   0.001   TYR L  92 
 PHE   0.013   0.002   PHE B 456 
 TRP   0.017   0.002   TRP L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 3336)
  covalent geometry    : angle       0.67892 ( 4544)
  SS BOND              : bond        0.00416 (    7)
  SS BOND              : angle       2.36846 (   14)
  hydrogen bonds       : bond        0.03364 (  114)
  hydrogen bonds       : angle       6.38544 (  285)
  link_BETA1-4         : bond        0.00323 (    2)
  link_BETA1-4         : angle       1.97821 (    6)
  link_NAG-ASN         : bond        0.00028 (    1)
  link_NAG-ASN         : angle       1.65748 (    3)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 TRP cc_start: 0.8306 (t60) cc_final: 0.8041 (t60)
REVERT: H   91 THR cc_start: 0.8170 (m) cc_final: 0.7905 (m)
REVERT: H  112 MET cc_start: 0.8409 (mpp) cc_final: 0.7987 (mpp)
REVERT: L   11 LEU cc_start: 0.8181 (mm) cc_final: 0.7881 (mm)
REVERT: L   17 GLU cc_start: 0.7095 (pm20) cc_final: 0.6337 (pm20)
  outliers start: 20
  outliers final: 15
  residues processed: 92
  average time/residue: 0.0745
  time to fit residues: 8.1399
Evaluate side-chains
  87 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   34 VAL
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  122 SER
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   59 ILE
Chi-restraints excluded: chain L residue   71 ASP
Chi-restraints excluded: chain L residue   92 TYR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 8 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 27 optimal weight:    8.9990
   chunk 17 optimal weight:    8.9990
   chunk 29 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 34 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN
** L  43 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 = 0.3850 r_free = 0.3850 target = 0.112399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.093996 restraints weight = 8704.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.096582 restraints weight = 5951.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.098381 restraints weight = 4545.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.099843 restraints weight = 3745.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.100805 restraints weight = 3198.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3346  Z= 0.131
  Angle     :  0.678   7.950   4567  Z= 0.338
  Chirality :  0.045   0.135    501
  Planarity :  0.005   0.047    588
  Dihedral  :  7.577  48.452    555
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 24.13 %
    Favored  : 70.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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: -0.80 (0.42), residues: 418
  helix: -2.53 (0.84), residues: 33
  sheet: -0.60 (0.40), residues: 155
  loop : -0.01 (0.44), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L  78 
 TYR   0.016   0.001   TYR H  80 
 PHE   0.022   0.002   PHE B 392 
 TRP   0.019   0.002   TRP L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3336)
  covalent geometry    : angle       0.66190 ( 4544)
  SS BOND              : bond        0.00169 (    7)
  SS BOND              : angle       2.30239 (   14)
  hydrogen bonds       : bond        0.03292 (  114)
  hydrogen bonds       : angle       6.25742 (  285)
  link_BETA1-4         : bond        0.00321 (    2)
  link_BETA1-4         : angle       2.04434 (    6)
  link_NAG-ASN         : bond        0.00026 (    1)
  link_NAG-ASN         : angle       1.60362 (    3)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  112 MET cc_start: 0.8391 (mpp) cc_final: 0.7887 (mpp)
REVERT: L   11 LEU cc_start: 0.8201 (mm) cc_final: 0.7980 (mm)
REVERT: L   17 GLU cc_start: 0.7284 (pm20) cc_final: 0.6554 (pm20)
  outliers start: 18
  outliers final: 14
  residues processed: 91
  average time/residue: 0.0726
  time to fit residues: 7.9574
Evaluate side-chains
  88 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue   34 VAL
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   59 ILE
Chi-restraints excluded: chain L residue   71 ASP
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 19 optimal weight:    8.9990
   chunk 0 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** L  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.110528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.092021 restraints weight = 8695.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.094489 restraints weight = 6011.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.096329 restraints weight = 4598.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.097673 restraints weight = 3773.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.098724 restraints weight = 3250.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   3346  Z= 0.236
  Angle     :  0.733   9.525   4567  Z= 0.370
  Chirality :  0.047   0.146    501
  Planarity :  0.005   0.048    588
  Dihedral  :  7.036  42.479    555
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 16.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 24.44 %
    Favored  : 69.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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: -1.02 (0.42), residues: 418
  helix: -2.55 (0.84), residues: 33
  sheet: -0.73 (0.40), residues: 154
  loop : -0.19 (0.43), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 346 
 TYR   0.013   0.001   TYR B 453 
 PHE   0.030   0.003   PHE B 392 
 TRP   0.020   0.002   TRP L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00529 ( 3336)
  covalent geometry    : angle       0.72263 ( 4544)
  SS BOND              : bond        0.00383 (    7)
  SS BOND              : angle       1.70980 (   14)
  hydrogen bonds       : bond        0.03797 (  114)
  hydrogen bonds       : angle       6.47833 (  285)
  link_BETA1-4         : bond        0.00412 (    2)
  link_BETA1-4         : angle       2.04685 (    6)
  link_NAG-ASN         : bond        0.00126 (    1)
  link_NAG-ASN         : angle       2.31353 (    3)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   38 ARG cc_start: 0.7914 (ttt180) cc_final: 0.7510 (ttp80)
REVERT: H   47 TRP cc_start: 0.8413 (t60) cc_final: 0.7882 (t60)
REVERT: H   91 THR cc_start: 0.8243 (m) cc_final: 0.7984 (m)
REVERT: H  112 MET cc_start: 0.8488 (mpp) cc_final: 0.7914 (mpp)
REVERT: L   11 LEU cc_start: 0.8288 (mm) cc_final: 0.8041 (mm)
REVERT: L   17 GLU cc_start: 0.7411 (pm20) cc_final: 0.6543 (pm20)
  outliers start: 19
  outliers final: 16
  residues processed: 86
  average time/residue: 0.0909
  time to fit residues: 9.0691
Evaluate side-chains
  88 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue   34 VAL
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   23 CYS
Chi-restraints excluded: chain L residue   59 ILE
Chi-restraints excluded: chain L residue   71 ASP
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  452 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0370
   chunk 28 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 12 optimal weight:    6.9990
   chunk 35 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 36 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0980
   chunk 40 optimal weight:    5.9990
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
** L  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.112910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.094538 restraints weight = 8782.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.097010 restraints weight = 6206.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.098854 restraints weight = 4783.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.100287 restraints weight = 3942.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.101294 restraints weight = 3385.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3346  Z= 0.123
  Angle     :  0.717   7.171   4567  Z= 0.355
  Chirality :  0.047   0.219    501
  Planarity :  0.005   0.048    588
  Dihedral  :  6.516  39.654    555
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 26.67 %
    Favored  : 69.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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: -0.87 (0.42), residues: 418
  helix: -2.61 (0.82), residues: 33
  sheet: -0.69 (0.40), residues: 155
  loop : -0.01 (0.45), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  84 
 TYR   0.010   0.001   TYR L  88 
 PHE   0.026   0.002   PHE B 392 
 TRP   0.035   0.002   TRP L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3336)
  covalent geometry    : angle       0.70466 ( 4544)
  SS BOND              : bond        0.00280 (    7)
  SS BOND              : angle       2.12300 (   14)
  hydrogen bonds       : bond        0.03401 (  114)
  hydrogen bonds       : angle       6.40941 (  285)
  link_BETA1-4         : bond        0.00453 (    2)
  link_BETA1-4         : angle       1.94987 (    6)
  link_NAG-ASN         : bond        0.00018 (    1)
  link_NAG-ASN         : angle       1.46533 (    3)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
REVERT: H   47 TRP cc_start: 0.8320 (t60) cc_final: 0.7760 (t60)
REVERT: H   91 THR cc_start: 0.8160 (m) cc_final: 0.7931 (m)
REVERT: H  112 MET cc_start: 0.8359 (mpp) cc_final: 0.7907 (mpp)
REVERT: L   17 GLU cc_start: 0.7226 (pm20) cc_final: 0.6545 (pm20)
  outliers start: 11
  outliers final: 11
  residues processed: 92
  average time/residue: 0.0794
  time to fit residues: 8.6174
Evaluate side-chains
  88 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   71 ASP
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain B residue  351 TYR
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   chunk 0 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
** L  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.109663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.090930 restraints weight = 8635.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.093199 restraints weight = 6019.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.095015 restraints weight = 4675.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.096239 restraints weight = 3866.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.097269 restraints weight = 3377.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   3346  Z= 0.265
  Angle     :  0.815  10.510   4567  Z= 0.414
  Chirality :  0.048   0.148    501
  Planarity :  0.006   0.047    588
  Dihedral  :  6.489  37.120    555
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 18.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 28.25 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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: -1.08 (0.42), residues: 418
  helix: -2.51 (0.84), residues: 33
  sheet: -0.85 (0.40), residues: 155
  loop : -0.18 (0.44), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  78 
 TYR   0.014   0.002   TYR B 453 
 PHE   0.028   0.003   PHE B 392 
 TRP   0.078   0.004   TRP L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00598 ( 3336)
  covalent geometry    : angle       0.79584 ( 4544)
  SS BOND              : bond        0.00381 (    7)
  SS BOND              : angle       2.78759 (   14)
  hydrogen bonds       : bond        0.04091 (  114)
  hydrogen bonds       : angle       6.62711 (  285)
  link_BETA1-4         : bond        0.00306 (    2)
  link_BETA1-4         : angle       2.01431 (    6)
  link_NAG-ASN         : bond        0.00183 (    1)
  link_NAG-ASN         : angle       2.49785 (    3)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: H   19 LYS cc_start: 0.7608 (ttpp) cc_final: 0.7374 (ttpp)
REVERT: H   38 ARG cc_start: 0.7937 (ttt180) cc_final: 0.6970 (ttt-90)
REVERT: H   46 GLU cc_start: 0.6831 (pm20) cc_final: 0.6372 (pm20)
REVERT: H   47 TRP cc_start: 0.8380 (t60) cc_final: 0.7991 (t60)
REVERT: H   91 THR cc_start: 0.8256 (m) cc_final: 0.7993 (m)
REVERT: H  112 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7936 (mpp)
REVERT: L   17 GLU cc_start: 0.7550 (pm20) cc_final: 0.6610 (pm20)
  outliers start: 16
  outliers final: 14
  residues processed: 81
  average time/residue: 0.0796
  time to fit residues: 7.6162
Evaluate side-chains
  87 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue   34 VAL
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  112 MET
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   59 ILE
Chi-restraints excluded: chain L residue   71 ASP
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 19 optimal weight:   10.0000
   chunk 32 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** L  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.111640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.093152 restraints weight = 8799.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.095566 restraints weight = 6198.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.097353 restraints weight = 4812.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.098411 restraints weight = 3991.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.099630 restraints weight = 3511.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3346  Z= 0.145
  Angle     :  0.732   8.184   4567  Z= 0.366
  Chirality :  0.046   0.142    501
  Planarity :  0.005   0.049    588
  Dihedral  :  6.042  34.337    555
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 28.57 %
    Favored  : 66.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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: -0.91 (0.42), residues: 418
  helix: -2.60 (0.82), residues: 33
  sheet: -0.69 (0.40), residues: 159
  loop : -0.05 (0.44), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  87 
 TYR   0.009   0.001   TYR L  88 
 PHE   0.025   0.002   PHE B 392 
 TRP   0.062   0.003   TRP L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 3336)
  covalent geometry    : angle       0.71961 ( 4544)
  SS BOND              : bond        0.00231 (    7)
  SS BOND              : angle       2.12792 (   14)
  hydrogen bonds       : bond        0.03566 (  114)
  hydrogen bonds       : angle       6.40452 (  285)
  link_BETA1-4         : bond        0.00240 (    2)
  link_BETA1-4         : angle       1.86851 (    6)
  link_NAG-ASN         : bond        0.00045 (    1)
  link_NAG-ASN         : angle       1.55731 (    3)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.6836 (pm20) cc_final: 0.6633 (pm20)
REVERT: H   47 TRP cc_start: 0.8188 (t60) cc_final: 0.7703 (t60)
REVERT: H  112 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7970 (mpp)
REVERT: L   17 GLU cc_start: 0.7470 (pm20) cc_final: 0.6649 (pm20)
REVERT: L   78 ARG cc_start: 0.8095 (ttp80) cc_final: 0.7784 (tmm160)
  outliers start: 14
  outliers final: 13
  residues processed: 84
  average time/residue: 0.0803
  time to fit residues: 7.9056
Evaluate side-chains
  89 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue   34 VAL
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  112 MET
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   71 ASP
Chi-restraints excluded: chain L residue   92 TYR
Chi-restraints excluded: chain L residue  107 ILE
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  430 THR
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  525 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** L  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.111630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.092950 restraints weight = 8906.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.095564 restraints weight = 6099.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.097444 restraints weight = 4672.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.098833 restraints weight = 3833.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.099874 restraints weight = 3291.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.3064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3346  Z= 0.146
  Angle     :  0.729   7.851   4567  Z= 0.364
  Chirality :  0.046   0.138    501
  Planarity :  0.005   0.049    588
  Dihedral  :  5.780  31.533    555
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 28.57 %
    Favored  : 66.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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: -0.92 (0.42), residues: 418
  helix: -2.63 (0.81), residues: 33
  sheet: -0.68 (0.40), residues: 161
  loop : -0.05 (0.45), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  87 
 TYR   0.009   0.001   TYR L  88 
 PHE   0.025   0.002   PHE B 392 
 TRP   0.060   0.003   TRP L  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 3336)
  covalent geometry    : angle       0.71733 ( 4544)
  SS BOND              : bond        0.00201 (    7)
  SS BOND              : angle       2.07691 (   14)
  hydrogen bonds       : bond        0.03580 (  114)
  hydrogen bonds       : angle       6.30235 (  285)
  link_BETA1-4         : bond        0.00237 (    2)
  link_BETA1-4         : angle       1.84228 (    6)
  link_NAG-ASN         : bond        0.00038 (    1)
  link_NAG-ASN         : angle       1.73871 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 829.18 seconds
wall clock time: 14 minutes 55.29 seconds (895.29 seconds total)