Starting phenix.real_space_refine
on Sat May 10 02:13:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dad_27270/05_2025/8dad_27270.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dad_27270/05_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_27270/05_2025/8dad_27270.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dad_27270/05_2025/8dad_27270.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dad_27270/05_2025/8dad_27270.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dad_27270/05_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-5687/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: 3.47, per 1000 atoms: 1.07
  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: 1.24
  Conformation dependent library (CDL) restraints added in 427.1 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: 0.48
  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: 0.83

  Time building geometry restraints manager: 1.08 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:             1.590
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.930
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.520
-------------------------------------------------------------------------------
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  : 0.344 
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: 0.2033
  time to fit residues: 18.5872
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  : 0.342 
-------------------------------------------------------------------------------
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 = 0.094088 restraints weight = 8757.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.096575 restraints weight = 6072.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.098439 restraints weight = 4698.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
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  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 TRP cc_start: 0.8077 (t60) cc_final: 0.7657 (t60)
REVERT: H  112 MET cc_start: 0.8242 (mpp) cc_final: 0.7095 (mpp)
REVERT: L   78 ARG cc_start: 0.8033 (ttp80) cc_final: 0.7798 (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: 0.1795
  time to fit residues: 18.4998
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  : 0.360 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 36 optimal weight:    9.9990
   chunk 8 optimal weight:    8.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.3823 r_free = 0.3823 target = 0.110834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.092180 restraints weight = 8644.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.094637 restraints weight = 6045.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.096454 restraints weight = 4661.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   3346  Z= 0.214
  Angle     :  0.735  10.854   4567  Z= 0.366
  Chirality :  0.047   0.161    501
  Planarity :  0.005   0.049    588
  Dihedral  :  9.881  67.143    555
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 23.81 %
    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 (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: -0.94 (0.42), residues: 418
  helix: -2.12 (0.97), residues: 33
  sheet: -0.78 (0.41), residues: 153
  loop : -0.13 (0.44), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP L  36 
 PHE   0.029   0.002   PHE B 392 
 TYR   0.011   0.001   TYR B 453 
 ARG   0.003   0.001   ARG B 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00001 (    1)
  link_NAG-ASN         : angle       2.07957 (    3)
  link_BETA1-4         : bond        0.00316 (    2)
  link_BETA1-4         : angle       2.00167 (    6)
  hydrogen bonds       : bond        0.03706 (  114)
  hydrogen bonds       : angle       6.60871 (  285)
  SS BOND              : bond        0.00312 (    7)
  SS BOND              : angle       2.92038 (   14)
  covalent geometry    : bond        0.00476 ( 3336)
  covalent geometry    : angle       0.71320 ( 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  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   38 ARG cc_start: 0.7889 (ttt180) cc_final: 0.7564 (ttt180)
REVERT: H   47 TRP cc_start: 0.8288 (t60) cc_final: 0.7841 (t60)
REVERT: L   17 GLU cc_start: 0.7378 (pm20) cc_final: 0.6533 (pm20)
  outliers start: 19
  outliers final: 12
  residues processed: 82
  average time/residue: 0.1890
  time to fit residues: 18.2614
Evaluate side-chains
  77 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
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  418 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:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 14 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 35 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3836 r_free = 0.3836 target = 0.111385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.093034 restraints weight = 8733.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.095479 restraints weight = 6099.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.097141 restraints weight = 4716.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
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      :  0.003   0.034   3346  Z= 0.147
  Angle     :  0.651   7.556   4567  Z= 0.325
  Chirality :  0.046   0.176    501
  Planarity :  0.005   0.048    588
  Dihedral  :  8.989  60.156    555
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 22.22 %
    Favored  : 72.38 %
  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: -0.91 (0.42), residues: 418
  helix: -2.39 (0.88), residues: 33
  sheet: -0.79 (0.40), residues: 160
  loop :  0.02 (0.44), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP L  36 
 PHE   0.022   0.002   PHE B 392 
 TYR   0.009   0.001   TYR L  92 
 ARG   0.004   0.000   ARG L  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00017 (    1)
  link_NAG-ASN         : angle       1.72683 (    3)
  link_BETA1-4         : bond        0.00320 (    2)
  link_BETA1-4         : angle       1.99090 (    6)
  hydrogen bonds       : bond        0.03359 (  114)
  hydrogen bonds       : angle       6.36138 (  285)
  SS BOND              : bond        0.00304 (    7)
  SS BOND              : angle       1.33152 (   14)
  covalent geometry    : bond        0.00333 ( 3336)
  covalent geometry    : angle       0.64315 ( 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
  96 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   38 ARG cc_start: 0.7888 (ttt180) cc_final: 0.7261 (ttt180)
REVERT: H   47 TRP cc_start: 0.8240 (t60) cc_final: 0.7729 (t60)
REVERT: H  112 MET cc_start: 0.8388 (mpp) cc_final: 0.7972 (mpp)
REVERT: L   11 LEU cc_start: 0.8253 (mm) cc_final: 0.8024 (mm)
REVERT: L   17 GLU cc_start: 0.7329 (pm20) cc_final: 0.6477 (pm20)
REVERT: L  101 GLN cc_start: 0.8123 (pm20) cc_final: 0.7820 (pm20)
REVERT: B  486 PHE cc_start: 0.8301 (t80) cc_final: 0.7932 (t80)
  outliers start: 17
  outliers final: 13
  residues processed: 89
  average time/residue: 0.1941
  time to fit residues: 20.1831
Evaluate side-chains
  80 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.0980
   chunk 29 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 3 optimal weight:    0.5980
   chunk 7 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3831 r_free = 0.3831 target = 0.111410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.092618 restraints weight = 8754.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.095226 restraints weight = 5933.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.097170 restraints weight = 4505.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3346  Z= 0.169
  Angle     :  0.723   8.563   4567  Z= 0.358
  Chirality :  0.046   0.129    501
  Planarity :  0.007   0.102    588
  Dihedral  :  8.456  54.884    555
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  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 (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: -2.36 (0.89), residues: 33
  sheet: -0.74 (0.40), residues: 160
  loop :  0.00 (0.44), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP L  36 
 PHE   0.015   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        0.00049 (    1)
  link_NAG-ASN         : angle       1.83242 (    3)
  link_BETA1-4         : bond        0.00365 (    2)
  link_BETA1-4         : angle       1.98133 (    6)
  hydrogen bonds       : bond        0.03432 (  114)
  hydrogen bonds       : angle       6.34503 (  285)
  SS BOND              : bond        0.00244 (    7)
  SS BOND              : angle       2.86894 (   14)
  covalent geometry    : bond        0.00384 ( 3336)
  covalent geometry    : angle       0.70188 ( 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
  93 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   38 ARG cc_start: 0.7761 (ttt180) cc_final: 0.7241 (ttp80)
REVERT: H   47 TRP cc_start: 0.8342 (t60) cc_final: 0.7649 (t60)
REVERT: H   72 ARG cc_start: 0.7988 (pmt-80) cc_final: 0.7536 (pmt-80)
REVERT: H   91 THR cc_start: 0.8375 (m) cc_final: 0.8129 (m)
REVERT: H  112 MET cc_start: 0.8442 (mpp) cc_final: 0.7931 (mpp)
REVERT: L   11 LEU cc_start: 0.8297 (mm) cc_final: 0.8084 (mm)
REVERT: L   17 GLU cc_start: 0.7391 (pm20) cc_final: 0.6540 (pm20)
REVERT: L   22 SER cc_start: 0.8242 (OUTLIER) cc_final: 0.8024 (p)
REVERT: L  101 GLN cc_start: 0.8114 (pm20) cc_final: 0.7634 (pm20)
  outliers start: 20
  outliers final: 17
  residues processed: 84
  average time/residue: 0.2009
  time to fit residues: 19.6317
Evaluate side-chains
  86 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
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   22 SER
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  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:    6.9990
   chunk 22 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 6 optimal weight:    8.9990
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 17 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 = 0.3831 r_free = 0.3831 target = 0.111142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.093105 restraints weight = 8931.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.095524 restraints weight = 6172.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.097354 restraints weight = 4756.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.2222

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= 0.147
  Angle     :  0.694   8.588   4567  Z= 0.345
  Chirality :  0.046   0.131    501
  Planarity :  0.006   0.093    588
  Dihedral  :  7.465  47.197    555
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 23.17 %
    Favored  : 70.79 %
  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: -2.54 (0.85), residues: 33
  sheet: -0.63 (0.41), residues: 157
  loop :  0.03 (0.44), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP L  36 
 PHE   0.012   0.002   PHE H  27 
 TYR   0.009   0.001   TYR L  92 
 ARG   0.004   0.000   ARG L  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00008 (    1)
  link_NAG-ASN         : angle       1.68244 (    3)
  link_BETA1-4         : bond        0.00377 (    2)
  link_BETA1-4         : angle       2.00241 (    6)
  hydrogen bonds       : bond        0.03436 (  114)
  hydrogen bonds       : angle       6.31100 (  285)
  SS BOND              : bond        0.00307 (    7)
  SS BOND              : angle       2.40084 (   14)
  covalent geometry    : bond        0.00337 ( 3336)
  covalent geometry    : angle       0.67784 ( 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: 19
    poor density    : 77
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   47 TRP cc_start: 0.8366 (t60) cc_final: 0.8165 (t60)
REVERT: H   72 ARG cc_start: 0.7956 (pmt-80) cc_final: 0.7701 (pmt-80)
REVERT: H  112 MET cc_start: 0.8457 (mpp) cc_final: 0.8022 (mpp)
REVERT: L   11 LEU cc_start: 0.8176 (mm) cc_final: 0.7963 (mm)
REVERT: L   17 GLU cc_start: 0.7225 (pm20) cc_final: 0.6436 (pm20)
REVERT: L   74 LEU cc_start: 0.6835 (mp) cc_final: 0.6595 (mp)
  outliers start: 19
  outliers final: 16
  residues processed: 85
  average time/residue: 0.1809
  time to fit residues: 18.2457
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  : 0.420 
-------------------------------------------------------------------------------
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   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:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 40 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 19 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.3812 r_free = 0.3812 target = 0.110796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.092368 restraints weight = 8571.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.094781 restraints weight = 5846.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.096630 restraints weight = 4460.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   3346  Z= 0.217
  Angle     :  0.698   6.472   4567  Z= 0.353
  Chirality :  0.046   0.135    501
  Planarity :  0.005   0.049    588
  Dihedral  :  6.901  42.554    555
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  7.30 %
    Allowed  : 22.22 %
    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: -0.97 (0.42), residues: 418
  helix: -2.64 (0.82), residues: 33
  sheet: -0.70 (0.40), residues: 162
  loop : -0.11 (0.45), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP L  36 
 PHE   0.017   0.002   PHE H  27 
 TYR   0.012   0.001   TYR L  88 
 ARG   0.003   0.000   ARG B 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00103 (    1)
  link_NAG-ASN         : angle       2.11693 (    3)
  link_BETA1-4         : bond        0.00271 (    2)
  link_BETA1-4         : angle       1.98595 (    6)
  hydrogen bonds       : bond        0.03659 (  114)
  hydrogen bonds       : angle       6.39032 (  285)
  SS BOND              : bond        0.00325 (    7)
  SS BOND              : angle       1.38461 (   14)
  covalent geometry    : bond        0.00488 ( 3336)
  covalent geometry    : angle       0.69003 ( 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
  99 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   38 ARG cc_start: 0.7856 (ttt180) cc_final: 0.7613 (ttp80)
REVERT: H   47 TRP cc_start: 0.8513 (t60) cc_final: 0.7791 (t60)
REVERT: H   72 ARG cc_start: 0.8168 (pmt-80) cc_final: 0.7875 (pmt-80)
REVERT: H  112 MET cc_start: 0.8490 (mpp) cc_final: 0.7941 (mpp)
REVERT: L   11 LEU cc_start: 0.8277 (mm) cc_final: 0.8050 (mm)
  outliers start: 23
  outliers final: 19
  residues processed: 87
  average time/residue: 0.1954
  time to fit residues: 19.8496
Evaluate side-chains
  91 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
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 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   57 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  351 TYR
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 2 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 24 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0570
   chunk 36 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.7098

-------------------------------------------------------------------------------
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 = 0.3839 r_free = 0.3839 target = 0.111686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.093679 restraints weight = 8539.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.096026 restraints weight = 5998.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.097749 restraints weight = 4669.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3346  Z= 0.136
  Angle     :  0.732  10.430   4567  Z= 0.360
  Chirality :  0.046   0.169    501
  Planarity :  0.007   0.108    588
  Dihedral  :  6.499  39.719    555
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  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: -0.74 (0.42), residues: 418
  helix: -2.64 (0.82), residues: 33
  sheet: -0.46 (0.43), residues: 147
  loop : -0.04 (0.43), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP L  36 
 PHE   0.018   0.002   PHE H  29 
 TYR   0.010   0.001   TYR L  88 
 ARG   0.006   0.001   ARG L  78 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00004 (    1)
  link_NAG-ASN         : angle       1.59448 (    3)
  link_BETA1-4         : bond        0.00245 (    2)
  link_BETA1-4         : angle       1.91934 (    6)
  hydrogen bonds       : bond        0.03369 (  114)
  hydrogen bonds       : angle       6.28967 (  285)
  SS BOND              : bond        0.00276 (    7)
  SS BOND              : angle       2.18095 (   14)
  covalent geometry    : bond        0.00317 ( 3336)
  covalent geometry    : angle       0.71905 ( 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
  105 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
REVERT: H   91 THR cc_start: 0.8243 (m) cc_final: 0.7999 (m)
REVERT: H  112 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8023 (mpp)
  outliers start: 19
  outliers final: 17
  residues processed: 94
  average time/residue: 0.1940
  time to fit residues: 21.4519
Evaluate side-chains
  89 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
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 H residue  112 MET
Chi-restraints excluded: chain L residue    2 ILE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 39 optimal weight:    0.2980
   chunk 3 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 36 optimal weight:    0.3980
   chunk 17 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3855 r_free = 0.3855 target = 0.112786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.094628 restraints weight = 8805.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.097089 restraints weight = 6228.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.098959 restraints weight = 4776.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   3346  Z= 0.141
  Angle     :  0.741   8.295   4567  Z= 0.375
  Chirality :  0.046   0.159    501
  Planarity :  0.005   0.054    588
  Dihedral  :  6.241  36.322    555
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 26.35 %
    Favored  : 67.94 %
  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: -0.81 (0.43), residues: 418
  helix: -2.76 (0.81), residues: 33
  sheet: -0.47 (0.42), residues: 149
  loop : -0.11 (0.44), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.003   TRP L  36 
 PHE   0.013   0.001   PHE H  29 
 TYR   0.010   0.001   TYR L  88 
 ARG   0.005   0.001   ARG H  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00026 (    1)
  link_NAG-ASN         : angle       1.50682 (    3)
  link_BETA1-4         : bond        0.00424 (    2)
  link_BETA1-4         : angle       1.96895 (    6)
  hydrogen bonds       : bond        0.03470 (  114)
  hydrogen bonds       : angle       6.31666 (  285)
  SS BOND              : bond        0.00345 (    7)
  SS BOND              : angle       1.92858 (   14)
  covalent geometry    : bond        0.00328 ( 3336)
  covalent geometry    : angle       0.73077 ( 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
  96 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: H  112 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7981 (mpp)
REVERT: L  101 GLN cc_start: 0.8141 (pm20) cc_final: 0.7869 (mp10)
  outliers start: 18
  outliers final: 16
  residues processed: 85
  average time/residue: 0.1805
  time to fit residues: 18.0717
Evaluate side-chains
  92 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0060
   chunk 24 optimal weight:    0.8980
   chunk 33 optimal weight:    9.9990
   chunk 18 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0670
   chunk 13 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.5536

-------------------------------------------------------------------------------
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 = 0.3857 r_free = 0.3857 target = 0.112650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.094751 restraints weight = 8655.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.097297 restraints weight = 6082.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.099182 restraints weight = 4653.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.2893

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     :  0.761  11.765   4567  Z= 0.379
  Chirality :  0.046   0.137    501
  Planarity :  0.005   0.052    588
  Dihedral  :  5.988  34.067    555
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 27.62 %
    Favored  : 66.35 %
  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: -0.83 (0.42), residues: 418
  helix: -2.73 (0.81), residues: 33
  sheet: -0.48 (0.42), residues: 147
  loop : -0.13 (0.43), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.069   0.003   TRP L  36 
 PHE   0.012   0.001   PHE H  27 
 TYR   0.010   0.001   TYR L  88 
 ARG   0.009   0.001   ARG H  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00011 (    1)
  link_NAG-ASN         : angle       1.47225 (    3)
  link_BETA1-4         : bond        0.00102 (    2)
  link_BETA1-4         : angle       1.86110 (    6)
  hydrogen bonds       : bond        0.03436 (  114)
  hydrogen bonds       : angle       6.32899 (  285)
  SS BOND              : bond        0.00174 (    7)
  SS BOND              : angle       2.14019 (   14)
  covalent geometry    : bond        0.00306 ( 3336)
  covalent geometry    : angle       0.74962 ( 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
  96 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.6604 (pm20) cc_final: 0.6354 (pm20)
REVERT: H   66 GLU cc_start: 0.6727 (pm20) cc_final: 0.6505 (pm20)
REVERT: H   91 THR cc_start: 0.8226 (m) cc_final: 0.7980 (m)
REVERT: H  112 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7947 (mpp)
REVERT: L   74 LEU cc_start: 0.6919 (mp) cc_final: 0.6660 (mp)
REVERT: L  101 GLN cc_start: 0.8158 (pm20) cc_final: 0.7883 (mp10)
  outliers start: 19
  outliers final: 17
  residues processed: 85
  average time/residue: 0.1695
  time to fit residues: 17.1748
Evaluate side-chains
  92 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
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    7 SER
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0970
   chunk 23 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.2182

-------------------------------------------------------------------------------
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 = 0.3835 r_free = 0.3835 target = 0.111356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.092765 restraints weight = 8756.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.095193 restraints weight = 6138.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.097039 restraints weight = 4773.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3346  Z= 0.164
  Angle     :  0.746   7.768   4567  Z= 0.375
  Chirality :  0.046   0.135    501
  Planarity :  0.005   0.051    588
  Dihedral  :  5.773  32.010    555
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  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 (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: -0.86 (0.43), residues: 418
  helix: -2.63 (0.82), residues: 33
  sheet: -0.65 (0.40), residues: 160
  loop : -0.00 (0.45), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.063   0.003   TRP L  36 
 PHE   0.015   0.002   PHE H  27 
 TYR   0.022   0.001   TYR H  80 
 ARG   0.008   0.001   ARG H  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00032 (    1)
  link_NAG-ASN         : angle       1.74683 (    3)
  link_BETA1-4         : bond        0.00233 (    2)
  link_BETA1-4         : angle       1.89472 (    6)
  hydrogen bonds       : bond        0.03537 (  114)
  hydrogen bonds       : angle       6.30005 (  285)
  SS BOND              : bond        0.00290 (    7)
  SS BOND              : angle       2.29811 (   14)
  covalent geometry    : bond        0.00381 ( 3336)
  covalent geometry    : angle       0.73258 ( 4544)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1566.35 seconds
wall clock time: 28 minutes 0.23 seconds (1680.23 seconds total)