Starting phenix.real_space_refine
on Wed Jul 23 23:38:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dad_27270/07_2025/8dad_27270.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dad_27270/07_2025/8dad_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dad_27270/07_2025/8dad_27270.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dad_27270/07_2025/8dad_27270.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dad_27270/07_2025/8dad_27270.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dad_27270/07_2025/8dad_27270.cif"
  }
  resolution = 3.85
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.044
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 5}
          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: 2.87, per 1000 atoms: 0.88
  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: 0.78
  Conformation dependent library (CDL) restraints added in 369.9 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: 0.40
  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: 0.80

  Time building geometry restraints manager: 0.94 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:             2.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.520
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.660
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.049   0.003   TRP L  36 
 PHE   0.013   0.002   PHE H  27 
 TYR   0.009   0.001   TYR L  92 
 ARG   0.004   0.001   ARG H  38 

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

*********************** 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  : 0.377 
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: 0.2123
  time to fit residues: 19.4196
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  : 0.324 
-------------------------------------------------------------------------------
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 34 optimal weight:    2.9990
   chunk 31 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 10 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 19 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3854 r_free = 0.3854 target = 0.112764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.094087 restraints weight = 8757.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.096574 restraints weight = 6072.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.098447 restraints weight = 4699.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.1155

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= 0.130
  Angle     :  0.677   7.194   4567  Z= 0.339
  Chirality :  0.047   0.145    501
  Planarity :  0.005   0.050    588
  Dihedral  : 10.590  73.259    556
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 24.13 %
    Favored  : 72.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.42), residues: 418
  helix: -2.08 (0.96), residues: 34
  sheet: -0.71 (0.41), residues: 158
  loop : -0.08 (0.44), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP L  36 
 PHE   0.031   0.002   PHE B 392 
 TYR   0.010   0.001   TYR L  92 
 ARG   0.003   0.001   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00155 (    1)
  link_NAG-ASN         : angle       1.33636 (    3)
  link_BETA1-4         : bond        0.00387 (    2)
  link_BETA1-4         : angle       2.21641 (    6)
  hydrogen bonds       : bond        0.03517 (  114)
  hydrogen bonds       : angle       6.79333 (  285)
  SS BOND              : bond        0.00353 (    7)
  SS BOND              : angle       1.76222 (   14)
  covalent geometry    : bond        0.00288 ( 3336)
  covalent geometry    : angle       0.66636 ( 4544)

*********************** 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
  91 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 TRP cc_start: 0.8076 (t60) cc_final: 0.7657 (t60)
REVERT: H  112 MET cc_start: 0.8241 (mpp) cc_final: 0.7091 (mpp)
REVERT: L   78 ARG cc_start: 0.8029 (ttp80) cc_final: 0.7796 (tmm160)
REVERT: L   80 GLU cc_start: 0.7273 (tt0) cc_final: 0.6976 (tt0)
  outliers start: 12
  outliers final: 6
  residues processed: 87
  average time/residue: 0.2005
  time to fit residues: 20.6186
Evaluate side-chains
  75 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  122 SER
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
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 13 optimal weight:   10.0000
   chunk 36 optimal weight:    8.9990
   chunk 8 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.9188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.110906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.092210 restraints weight = 8661.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.094645 restraints weight = 6054.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.096485 restraints weight = 4684.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   3346  Z= 0.212
  Angle     :  0.731   9.936   4567  Z= 0.365
  Chirality :  0.047   0.140    501
  Planarity :  0.005   0.049    588
  Dihedral  :  9.871  67.171    555
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 23.49 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.43), residues: 418
  helix: -2.12 (0.97), residues: 33
  sheet: -0.77 (0.41), residues: 153
  loop : -0.10 (0.44), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP L  36 
 PHE   0.028   0.002   PHE B 392 
 TYR   0.011   0.001   TYR B 453 
 ARG   0.003   0.000   ARG B 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00022 (    1)
  link_NAG-ASN         : angle       2.07303 (    3)
  link_BETA1-4         : bond        0.00220 (    2)
  link_BETA1-4         : angle       1.95998 (    6)
  hydrogen bonds       : bond        0.03686 (  114)
  hydrogen bonds       : angle       6.61074 (  285)
  SS BOND              : bond        0.00273 (    7)
  SS BOND              : angle       2.85325 (   14)
  covalent geometry    : bond        0.00471 ( 3336)
  covalent geometry    : angle       0.71041 ( 4544)

*********************** 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
  92 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   38 ARG cc_start: 0.7877 (ttt180) cc_final: 0.7515 (ttt180)
REVERT: H   47 TRP cc_start: 0.8288 (t60) cc_final: 0.7842 (t60)
REVERT: L   17 GLU cc_start: 0.7377 (pm20) cc_final: 0.6531 (pm20)
  outliers start: 19
  outliers final: 11
  residues processed: 83
  average time/residue: 0.1878
  time to fit residues: 18.2981
Evaluate side-chains
  76 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
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   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 20 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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 = 0.3823 r_free = 0.3823 target = 0.110529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.091242 restraints weight = 8789.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.093792 restraints weight = 5955.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.095724 restraints weight = 4551.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3346  Z= 0.180
  Angle     :  0.663   7.486   4567  Z= 0.332
  Chirality :  0.046   0.225    501
  Planarity :  0.005   0.049    588
  Dihedral  :  9.102  61.091    555
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 23.81 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.42), residues: 418
  helix: -2.31 (0.89), residues: 33
  sheet: -0.78 (0.41), residues: 154
  loop : -0.11 (0.43), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP L  36 
 PHE   0.024   0.002   PHE B 392 
 TYR   0.010   0.001   TYR L  92 
 ARG   0.005   0.000   ARG L  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00059 (    1)
  link_NAG-ASN         : angle       1.94492 (    3)
  link_BETA1-4         : bond        0.00299 (    2)
  link_BETA1-4         : angle       1.99651 (    6)
  hydrogen bonds       : bond        0.03452 (  114)
  hydrogen bonds       : angle       6.39301 (  285)
  SS BOND              : bond        0.00383 (    7)
  SS BOND              : angle       1.37003 (   14)
  covalent geometry    : bond        0.00408 ( 3336)
  covalent geometry    : angle       0.65477 ( 4544)

*********************** 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: 16
    poor density    : 75
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   38 ARG cc_start: 0.7877 (ttt180) cc_final: 0.6799 (ttt180)
REVERT: H   47 TRP cc_start: 0.8302 (t60) cc_final: 0.7812 (t60)
REVERT: H   72 ARG cc_start: 0.8128 (pmt-80) cc_final: 0.7859 (pmt-80)
REVERT: H  112 MET cc_start: 0.8425 (mpp) cc_final: 0.7934 (mpp)
REVERT: L   11 LEU cc_start: 0.8326 (mm) cc_final: 0.8059 (mm)
REVERT: L   17 GLU cc_start: 0.7467 (pm20) cc_final: 0.6602 (pm20)
REVERT: L   37 TYR cc_start: 0.8702 (m-80) cc_final: 0.8499 (m-80)
  outliers start: 16
  outliers final: 14
  residues processed: 84
  average time/residue: 0.2062
  time to fit residues: 20.3071
Evaluate side-chains
  80 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
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  351 TYR
Chi-restraints excluded: chain B residue  391 CYS
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 16 optimal weight:    0.0870
   chunk 29 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.7358

-------------------------------------------------------------------------------
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 = 0.3841 r_free = 0.3841 target = 0.111882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.092690 restraints weight = 8712.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.095368 restraints weight = 5919.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.097275 restraints weight = 4471.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3346  Z= 0.130
  Angle     :  0.701   8.472   4567  Z= 0.344
  Chirality :  0.045   0.129    501
  Planarity :  0.006   0.094    588
  Dihedral  :  8.344  54.211    555
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 24.76 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.42), residues: 418
  helix: -2.33 (0.89), residues: 33
  sheet: -0.72 (0.40), residues: 158
  loop :  0.03 (0.45), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP L  36 
 PHE   0.013   0.002   PHE B 456 
 TYR   0.009   0.001   TYR L  92 
 ARG   0.007   0.001   ARG L  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00004 (    1)
  link_NAG-ASN         : angle       1.59704 (    3)
  link_BETA1-4         : bond        0.00190 (    2)
  link_BETA1-4         : angle       1.96960 (    6)
  hydrogen bonds       : bond        0.03276 (  114)
  hydrogen bonds       : angle       6.27936 (  285)
  SS BOND              : bond        0.00168 (    7)
  SS BOND              : angle       2.50544 (   14)
  covalent geometry    : bond        0.00300 ( 3336)
  covalent geometry    : angle       0.68411 ( 4544)

*********************** 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
  97 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   38 ARG cc_start: 0.7661 (ttt180) cc_final: 0.7045 (ttt180)
REVERT: H   47 TRP cc_start: 0.8242 (t60) cc_final: 0.8033 (t60)
REVERT: H  112 MET cc_start: 0.8371 (mpp) cc_final: 0.7912 (mpp)
REVERT: L   11 LEU cc_start: 0.8272 (mm) cc_final: 0.8057 (mm)
REVERT: L   17 GLU cc_start: 0.7381 (pm20) cc_final: 0.6562 (pm20)
REVERT: L   22 SER cc_start: 0.8251 (OUTLIER) cc_final: 0.7998 (p)
REVERT: L   37 TYR cc_start: 0.8682 (m-80) cc_final: 0.8474 (m-10)
REVERT: B  486 PHE cc_start: 0.8292 (t80) cc_final: 0.7860 (t80)
  outliers start: 17
  outliers final: 14
  residues processed: 87
  average time/residue: 0.1955
  time to fit residues: 19.8931
Evaluate side-chains
  86 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
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 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   22 SER
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  430 THR
Chi-restraints excluded: chain B residue  452 LEU
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 7 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.1986

-------------------------------------------------------------------------------
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 = 0.3828 r_free = 0.3828 target = 0.110868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.092772 restraints weight = 8937.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.095219 restraints weight = 6254.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.097016 restraints weight = 4806.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3346  Z= 0.159
  Angle     :  0.693   8.201   4567  Z= 0.344
  Chirality :  0.045   0.131    501
  Planarity :  0.006   0.102    588
  Dihedral  :  7.546  47.877    555
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  6.67 %
    Allowed  : 23.81 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.42), residues: 418
  helix: -2.38 (0.86), residues: 33
  sheet: -0.67 (0.40), residues: 159
  loop :  0.05 (0.44), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP L  36 
 PHE   0.014   0.002   PHE H  27 
 TYR   0.013   0.001   TYR H  80 
 ARG   0.005   0.000   ARG L  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00010 (    1)
  link_NAG-ASN         : angle       1.78503 (    3)
  link_BETA1-4         : bond        0.00332 (    2)
  link_BETA1-4         : angle       2.01571 (    6)
  hydrogen bonds       : bond        0.03353 (  114)
  hydrogen bonds       : angle       6.23972 (  285)
  SS BOND              : bond        0.00321 (    7)
  SS BOND              : angle       2.40361 (   14)
  covalent geometry    : bond        0.00369 ( 3336)
  covalent geometry    : angle       0.67660 ( 4544)

*********************** 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
  96 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 TRP cc_start: 0.8376 (t60) cc_final: 0.8161 (t60)
REVERT: H   72 ARG cc_start: 0.7894 (pmt-80) cc_final: 0.7334 (pmt-80)
REVERT: H  112 MET cc_start: 0.8437 (mpp) cc_final: 0.7982 (mpp)
REVERT: L   11 LEU cc_start: 0.8196 (mm) cc_final: 0.7978 (mm)
REVERT: L   17 GLU cc_start: 0.7177 (pm20) cc_final: 0.6319 (pm20)
  outliers start: 21
  outliers final: 17
  residues processed: 85
  average time/residue: 0.1825
  time to fit residues: 18.3765
Evaluate side-chains
  87 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
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   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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 22 optimal weight:    0.1980
   chunk 2 optimal weight:    0.8980
   chunk 19 optimal weight:   30.0000
   chunk 1 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3841 r_free = 0.3841 target = 0.111844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.093965 restraints weight = 8685.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.096397 restraints weight = 6121.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.098172 restraints weight = 4722.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3346  Z= 0.135
  Angle     :  0.681   9.680   4567  Z= 0.336
  Chirality :  0.046   0.148    501
  Planarity :  0.006   0.105    588
  Dihedral  :  6.885  42.700    555
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 26.03 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.43), residues: 418
  helix: -2.53 (0.83), residues: 33
  sheet: -0.50 (0.41), residues: 157
  loop : -0.03 (0.45), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP L  36 
 PHE   0.011   0.001   PHE H  27 
 TYR   0.011   0.001   TYR L  88 
 ARG   0.008   0.001   ARG H  84 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00025 (    1)
  link_NAG-ASN         : angle       1.57778 (    3)
  link_BETA1-4         : bond        0.00287 (    2)
  link_BETA1-4         : angle       2.00810 (    6)
  hydrogen bonds       : bond        0.03384 (  114)
  hydrogen bonds       : angle       6.25155 (  285)
  SS BOND              : bond        0.00229 (    7)
  SS BOND              : angle       1.38520 (   14)
  covalent geometry    : bond        0.00314 ( 3336)
  covalent geometry    : angle       0.67306 ( 4544)

*********************** 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
  95 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   72 ARG cc_start: 0.7944 (pmt-80) cc_final: 0.7488 (pmt-80)
REVERT: H  112 MET cc_start: 0.8391 (mpp) cc_final: 0.7986 (mpp)
REVERT: L   17 GLU cc_start: 0.7277 (pm20) cc_final: 0.6461 (pm20)
  outliers start: 15
  outliers final: 14
  residues processed: 87
  average time/residue: 0.1797
  time to fit residues: 18.6274
Evaluate side-chains
  85 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue   34 VAL
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   92 TYR
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
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 2 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0870
   chunk 24 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 36 optimal weight:   10.0000
   chunk 34 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 19 optimal weight:    8.9990
   overall best weight:    0.8360

-------------------------------------------------------------------------------
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 = 0.3850 r_free = 0.3850 target = 0.112666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.094392 restraints weight = 8538.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.096756 restraints weight = 5942.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.098722 restraints weight = 4603.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3346  Z= 0.138
  Angle     :  0.707   6.672   4567  Z= 0.351
  Chirality :  0.046   0.151    501
  Planarity :  0.006   0.079    588
  Dihedral  :  6.354  38.702    555
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 26.67 %
    Favored  : 68.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.42), residues: 418
  helix: -2.46 (0.84), residues: 33
  sheet: -0.51 (0.41), residues: 155
  loop :  0.02 (0.44), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP L  36 
 PHE   0.012   0.001   PHE H  27 
 TYR   0.013   0.001   TYR H  80 
 ARG   0.008   0.001   ARG H  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00022 (    1)
  link_NAG-ASN         : angle       1.57810 (    3)
  link_BETA1-4         : bond        0.00303 (    2)
  link_BETA1-4         : angle       2.00312 (    6)
  hydrogen bonds       : bond        0.03380 (  114)
  hydrogen bonds       : angle       6.33638 (  285)
  SS BOND              : bond        0.00236 (    7)
  SS BOND              : angle       2.39060 (   14)
  covalent geometry    : bond        0.00324 ( 3336)
  covalent geometry    : angle       0.69124 ( 4544)

*********************** 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
  96 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  112 MET cc_start: 0.8407 (mpp) cc_final: 0.7950 (mpp)
REVERT: L   17 GLU cc_start: 0.7393 (pm20) cc_final: 0.6589 (pm20)
  outliers start: 16
  outliers final: 13
  residues processed: 87
  average time/residue: 0.1674
  time to fit residues: 17.4662
Evaluate side-chains
  88 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   34 VAL
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   57 THR
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  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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 16 optimal weight:    0.1980
   chunk 35 optimal weight:    0.0040
   chunk 39 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0470
   overall best weight:    0.4090

-------------------------------------------------------------------------------
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 = 0.3864 r_free = 0.3864 target = 0.113459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.095200 restraints weight = 8855.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.097731 restraints weight = 6065.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.099629 restraints weight = 4640.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3346  Z= 0.131
  Angle     :  0.746  11.100   4567  Z= 0.373
  Chirality :  0.047   0.153    501
  Planarity :  0.006   0.067    588
  Dihedral  :  6.149  35.411    555
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 28.89 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.43), residues: 418
  helix: -2.62 (0.83), residues: 33
  sheet: -0.35 (0.42), residues: 147
  loop : -0.05 (0.44), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.003   TRP L  36 
 PHE   0.017   0.002   PHE H  29 
 TYR   0.008   0.001   TYR L  88 
 ARG   0.008   0.001   ARG H  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00070 (    1)
  link_NAG-ASN         : angle       1.36906 (    3)
  link_BETA1-4         : bond        0.00166 (    2)
  link_BETA1-4         : angle       1.94907 (    6)
  hydrogen bonds       : bond        0.03446 (  114)
  hydrogen bonds       : angle       6.35870 (  285)
  SS BOND              : bond        0.00272 (    7)
  SS BOND              : angle       2.01850 (   14)
  covalent geometry    : bond        0.00303 ( 3336)
  covalent geometry    : angle       0.73541 ( 4544)

*********************** 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
  97 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 TRP cc_start: 0.7909 (t60) cc_final: 0.7252 (t60)
REVERT: H   91 THR cc_start: 0.8264 (m) cc_final: 0.8011 (m)
REVERT: H  112 MET cc_start: 0.8330 (mpp) cc_final: 0.7930 (mpp)
REVERT: B  486 PHE cc_start: 0.8327 (t80) cc_final: 0.7983 (t80)
  outliers start: 13
  outliers final: 13
  residues processed: 88
  average time/residue: 0.1966
  time to fit residues: 20.1928
Evaluate side-chains
  92 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   27 PHE
Chi-restraints excluded: chain H residue   34 VAL
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   92 TYR
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
Chi-restraints excluded: chain B residue  452 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 17 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0670
   chunk 18 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0970
   chunk 16 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5116

-------------------------------------------------------------------------------
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 = 0.3869 r_free = 0.3869 target = 0.113815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.095731 restraints weight = 8593.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.098308 restraints weight = 5856.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.100184 restraints weight = 4448.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.2793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3346  Z= 0.126
  Angle     :  0.719   7.515   4567  Z= 0.358
  Chirality :  0.046   0.138    501
  Planarity :  0.006   0.054    588
  Dihedral  :  5.737  32.636    555
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 28.57 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.43), residues: 418
  helix: -2.61 (0.83), residues: 33
  sheet: -0.47 (0.41), residues: 152
  loop : -0.02 (0.44), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.003   TRP L  36 
 PHE   0.012   0.001   PHE B 392 
 TYR   0.008   0.001   TYR L  88 
 ARG   0.006   0.001   ARG H  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00065 (    1)
  link_NAG-ASN         : angle       1.40026 (    3)
  link_BETA1-4         : bond        0.00254 (    2)
  link_BETA1-4         : angle       1.91459 (    6)
  hydrogen bonds       : bond        0.03373 (  114)
  hydrogen bonds       : angle       6.30556 (  285)
  SS BOND              : bond        0.00158 (    7)
  SS BOND              : angle       2.05508 (   14)
  covalent geometry    : bond        0.00295 ( 3336)
  covalent geometry    : angle       0.70728 ( 4544)

********************** 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
  95 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 LYS cc_start: 0.7565 (ttpp) cc_final: 0.7139 (ttmm)
REVERT: H   46 GLU cc_start: 0.6550 (pm20) cc_final: 0.6293 (pm20)
REVERT: H   72 ARG cc_start: 0.7999 (pmt-80) cc_final: 0.7680 (pmt-80)
REVERT: H  112 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7867 (mpp)
REVERT: L   83 ASP cc_start: 0.7993 (m-30) cc_final: 0.7390 (m-30)
  outliers start: 15
  outliers final: 13
  residues processed: 86
  average time/residue: 0.1908
  time to fit residues: 19.3778
Evaluate side-chains
  90 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
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  112 MET
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   71 ASP
Chi-restraints excluded: chain L residue   92 TYR
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 24 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 23 optimal weight:    0.1980
   chunk 2 optimal weight:    6.9990
   chunk 18 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.8386

-------------------------------------------------------------------------------
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 = 0.3788 r_free = 0.3788 target = 0.109039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.090237 restraints weight = 8912.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.092537 restraints weight = 6236.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.094304 restraints weight = 4849.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   3346  Z= 0.218
  Angle     :  0.766   7.767   4567  Z= 0.391
  Chirality :  0.047   0.151    501
  Planarity :  0.005   0.048    588
  Dihedral  :  5.961  30.309    555
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 27.62 %
    Favored  : 67.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.42), residues: 418
  helix: -2.52 (0.85), residues: 33
  sheet: -0.60 (0.41), residues: 162
  loop : -0.23 (0.44), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.069   0.005   TRP L  36 
 PHE   0.019   0.002   PHE H  27 
 TYR   0.012   0.001   TYR B 453 
 ARG   0.006   0.001   ARG H  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00099 (    1)
  link_NAG-ASN         : angle       2.04213 (    3)
  link_BETA1-4         : bond        0.00290 (    2)
  link_BETA1-4         : angle       1.99775 (    6)
  hydrogen bonds       : bond        0.03777 (  114)
  hydrogen bonds       : angle       6.49154 (  285)
  SS BOND              : bond        0.00416 (    7)
  SS BOND              : angle       2.21627 (   14)
  covalent geometry    : bond        0.00497 ( 3336)
  covalent geometry    : angle       0.75314 ( 4544)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1895.34 seconds
wall clock time: 33 minutes 49.35 seconds (2029.35 seconds total)