Starting phenix.real_space_refine
on Wed Jul 23 12:29:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ru8_24699/07_2025/7ru8_24699.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ru8_24699/07_2025/7ru8_24699.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ru8_24699/07_2025/7ru8_24699.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ru8_24699/07_2025/7ru8_24699.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ru8_24699/07_2025/7ru8_24699.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ru8_24699/07_2025/7ru8_24699.cif"
  }
  resolution = 3.8
  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=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    2031      2.51       5
     N     532      2.21       5
     O     620      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 3198
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "H"
      Number of atoms: 956
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 956
          Classifications: {'peptide': 124}
          Link IDs: {'PTRANS': 4, 'TRANS': 119}
    Chain: "L"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 812
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101}
    Chain: "C"
      Number of atoms: 1388
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1388
          Classifications: {'peptide': 174}
          Link IDs: {'PTRANS': 9, 'TRANS': 164}
          Chain breaks: 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
    Chain: "L"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.54, per 1000 atoms: 1.11
  Number of scatterers: 3198
  At special positions: 0
  Unit cell: (56.65, 75.19, 107.12, 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      15     16.00
     O     620      8.00
     N     532      7.00
     C    2031      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  99 " - pdb=" SG  CYS H 100D" distance=2.02
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.02

  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-ASN
      " NAG A   1 " - " ASN C 343 "
      " NAG L 201 " - " ASN L  28 "
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 353.1 milliseconds
  

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  742

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 8 sheets defined
      11.4% alpha, 28.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'H' and resid 83 through 87
    Processing helix  chain 'L' and resid 79 through 83
    Processing helix  chain 'C' and resid 337 through 343
    Processing helix  chain 'C' and resid 365 through 370
    Processing helix  chain 'C' and resid 405 through 410
      removed outlier: 4.494A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'C' and resid 438 through 443
    Processing helix  chain 'C' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 59
      removed outlier: 5.550A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 96 through 100
    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 12
      removed outlier: 6.826A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.916A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.584A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 357
    Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454

    108 hydrogen bonds defined for protein.
    249 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: 1.35

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.18 -     1.32: 623
        1.32 -     1.45: 1156
        1.45 -     1.59: 1469
        1.59 -     1.73: 10
        1.73 -     1.87: 17
  Bond restraints: 3275
  Sorted by residual:
  bond pdb=" CB  LEU C 387 "
       pdb=" CG  LEU C 387 "
    ideal  model  delta    sigma   weight residual
    1.530  1.634 -0.104 2.00e-02 2.50e+03 2.72e+01
  bond pdb=" CG  PHE C 515 "
       pdb=" CD2 PHE C 515 "
    ideal  model  delta    sigma   weight residual
    1.384  1.489 -0.105 2.10e-02 2.27e+03 2.51e+01
  bond pdb=" CD  ARG L  96 "
       pdb=" NE  ARG L  96 "
    ideal  model  delta    sigma   weight residual
    1.458  1.390  0.068 1.40e-02 5.10e+03 2.37e+01
  bond pdb=" CG  PHE C 515 "
       pdb=" CD1 PHE C 515 "
    ideal  model  delta    sigma   weight residual
    1.384  1.486 -0.102 2.10e-02 2.27e+03 2.36e+01
  bond pdb=" CG  PHE C 429 "
       pdb=" CD2 PHE C 429 "
    ideal  model  delta    sigma   weight residual
    1.384  1.486 -0.102 2.10e-02 2.27e+03 2.34e+01
  ... (remaining 3270 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 3844
        2.57 -     5.14: 506
        5.14 -     7.71: 78
        7.71 -    10.27: 12
       10.27 -    12.84: 3
  Bond angle restraints: 4443
  Sorted by residual:
  angle pdb=" N   SER L  30 "
        pdb=" CA  SER L  30 "
        pdb=" C   SER L  30 "
      ideal   model   delta    sigma   weight residual
     111.28  119.73   -8.45 1.09e+00 8.42e-01 6.01e+01
  angle pdb=" C   SER C 383 "
        pdb=" N   PRO C 384 "
        pdb=" CA  PRO C 384 "
      ideal   model   delta    sigma   weight residual
     119.56  126.92   -7.36 1.01e+00 9.80e-01 5.31e+01
  angle pdb=" N   ARG H  94 "
        pdb=" CA  ARG H  94 "
        pdb=" C   ARG H  94 "
      ideal   model   delta    sigma   weight residual
     113.17  122.27   -9.10 1.26e+00 6.30e-01 5.21e+01
  angle pdb=" C   ASN C 487 "
        pdb=" N   CYS C 488 "
        pdb=" CA  CYS C 488 "
      ideal   model   delta    sigma   weight residual
     121.69  134.53  -12.84 1.85e+00 2.92e-01 4.82e+01
  angle pdb=" N   PRO H  41 "
        pdb=" CA  PRO H  41 "
        pdb=" C   PRO H  41 "
      ideal   model   delta    sigma   weight residual
     111.26  100.42   10.84 1.63e+00 3.76e-01 4.42e+01
  ... (remaining 4438 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.06: 1885
       17.06 -    34.12: 53
       34.12 -    51.19: 21
       51.19 -    68.25: 7
       68.25 -    85.31: 3
  Dihedral angle restraints: 1969
    sinusoidal: 799
      harmonic: 1170
  Sorted by residual:
  dihedral pdb=" CB  CYS C 480 "
           pdb=" SG  CYS C 480 "
           pdb=" SG  CYS C 488 "
           pdb=" CB  CYS C 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  127.21  -34.21     1      1.00e+01 1.00e-02 1.66e+01
  dihedral pdb=" N   ILE H  31 "
           pdb=" C   ILE H  31 "
           pdb=" CA  ILE H  31 "
           pdb=" CB  ILE H  31 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  131.51   -8.11     0      2.50e+00 1.60e-01 1.05e+01
  dihedral pdb=" C   ARG L  96 "
           pdb=" N   ARG L  96 "
           pdb=" CA  ARG L  96 "
           pdb=" CB  ARG L  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.72   -7.88     0      2.50e+00 1.60e-01 9.92e+00
  ... (remaining 1966 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.103: 354
       0.103 -    0.205: 97
       0.205 -    0.307: 26
       0.307 -    0.409: 4
       0.409 -    0.511: 6
  Chirality restraints: 487
  Sorted by residual:
  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   -2.56    0.16 2.00e-02 2.50e+03 6.51e+01
  chirality pdb=" C1  NAG L 201 "
            pdb=" ND2 ASN L  28 "
            pdb=" C2  NAG L 201 "
            pdb=" O5  NAG L 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.91    0.51 2.00e-01 2.50e+01 6.53e+00
  chirality pdb=" CG  LEU C 387 "
            pdb=" CB  LEU C 387 "
            pdb=" CD1 LEU C 387 "
            pdb=" CD2 LEU C 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -3.09    0.51 2.00e-01 2.50e+01 6.38e+00
  ... (remaining 484 not shown)

  Planarity restraints: 567
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN L  28 "    0.061 2.00e-02 2.50e+03   6.58e-02 5.41e+01
        pdb=" CG  ASN L  28 "   -0.025 2.00e-02 2.50e+03
        pdb=" OD1 ASN L  28 "   -0.010 2.00e-02 2.50e+03
        pdb=" ND2 ASN L  28 "   -0.105 2.00e-02 2.50e+03
        pdb=" C1  NAG L 201 "    0.079 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 489 "    0.086 2.00e-02 2.50e+03   4.50e-02 4.04e+01
        pdb=" CG  TYR C 489 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 489 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 489 "   -0.031 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 489 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 489 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 489 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR C 489 "    0.062 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  47 "   -0.077 2.00e-02 2.50e+03   3.89e-02 3.79e+01
        pdb=" CG  TRP H  47 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  47 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  47 "    0.040 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  47 "    0.013 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  47 "    0.009 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  47 "    0.057 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  47 "   -0.034 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  47 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  47 "   -0.049 2.00e-02 2.50e+03
  ... (remaining 564 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.86: 1160
        2.86 -     3.37: 2899
        3.37 -     3.88: 5523
        3.88 -     4.39: 6414
        4.39 -     4.90: 10245
  Nonbonded interactions: 26241
  Sorted by model distance:
  nonbonded pdb=" N   VAL C 350 "
            pdb=" O   VAL C 350 "
     model   vdw
     2.356 2.496
  nonbonded pdb=" C   SER C 349 "
            pdb=" O   VAL C 350 "
     model   vdw
     2.474 3.270
  nonbonded pdb=" N   TYR H  32 "
            pdb=" O   TYR H  32 "
     model   vdw
     2.478 2.496
  nonbonded pdb=" N   PHE C 429 "
            pdb=" O   PHE C 429 "
     model   vdw
     2.504 2.496
  nonbonded pdb=" N   ALA H  40 "
            pdb=" O   ALA H  40 "
     model   vdw
     2.504 2.496
  ... (remaining 26236 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.230
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
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      :  0.022   0.125   3284  Z= 1.133
  Angle     :  1.877  12.843   4464  Z= 1.222
  Chirality :  0.116   0.511    487
  Planarity :  0.009   0.045    565
  Dihedral  : 10.389  85.311   1209
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 1.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.23 (0.41), residues: 395
  helix: -4.33 (0.37), residues: 21
  sheet:  0.28 (0.44), residues: 134
  loop :  0.10 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.077   0.017   TRP H  47 
 PHE   0.033   0.007   PHE C 429 
 TYR   0.086   0.009   TYR C 489 
 ARG   0.006   0.001   ARG C 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.07511 (    2)
  link_NAG-ASN         : angle       4.05566 (    6)
  link_BETA1-4         : bond        0.05856 (    1)
  link_BETA1-4         : angle       4.64772 (    3)
  hydrogen bonds       : bond        0.16458 (  104)
  hydrogen bonds       : angle       9.49181 (  249)
  SS BOND              : bond        0.00837 (    6)
  SS BOND              : angle       2.72365 (   12)
  covalent geometry    : bond        0.02183 ( 3275)
  covalent geometry    : angle       1.86675 ( 4443)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   13 LYS cc_start: 0.2506 (mttt) cc_final: 0.1758 (mtpp)
REVERT: L    2 ILE cc_start: 0.7216 (mt) cc_final: 0.6844 (mt)
REVERT: C  424 LYS cc_start: 0.8356 (tptt) cc_final: 0.7692 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.2685
  time to fit residues: 30.6442
Evaluate side-chains
  49 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 29 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0030
   chunk 19 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0000
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.3594

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

Flipped N/Q/H residues before XYZ refinement:
L  89 GLN
C 501 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.083540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.077756 restraints weight = 14722.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.079311 restraints weight = 7825.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.080316 restraints weight = 4723.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3284  Z= 0.163
  Angle     :  0.791   7.427   4464  Z= 0.421
  Chirality :  0.048   0.138    487
  Planarity :  0.005   0.041    565
  Dihedral  :  5.993  30.156    510
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 11.92 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -0.33 (0.43), residues: 395
  helix: -3.47 (0.81), residues: 21
  sheet:  0.41 (0.50), residues: 124
  loop : -0.19 (0.39), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP H  47 
 PHE   0.033   0.002   PHE L  71 
 TYR   0.023   0.002   TYR C 489 
 ARG   0.004   0.001   ARG C 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00157 (    2)
  link_NAG-ASN         : angle       3.37016 (    6)
  link_BETA1-4         : bond        0.00135 (    1)
  link_BETA1-4         : angle       1.65816 (    3)
  hydrogen bonds       : bond        0.03959 (  104)
  hydrogen bonds       : angle       7.36341 (  249)
  SS BOND              : bond        0.00302 (    6)
  SS BOND              : angle       1.29045 (   12)
  covalent geometry    : bond        0.00354 ( 3275)
  covalent geometry    : angle       0.77918 ( 4443)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 1.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   13 LYS cc_start: 0.2735 (mttt) cc_final: 0.2137 (tttm)
REVERT: C  353 TRP cc_start: 0.6183 (m-90) cc_final: 0.5849 (m-90)
  outliers start: 7
  outliers final: 4
  residues processed: 63
  average time/residue: 0.1853
  time to fit residues: 14.0845
Evaluate side-chains
  51 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   62 PHE
Chi-restraints excluded: chain C residue  351 TYR
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  503 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 11 optimal weight:    0.2980
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
H   1 GLN
C 481 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.078435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.072003 restraints weight = 14166.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.073632 restraints weight = 7578.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.074634 restraints weight = 4585.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.4550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3284  Z= 0.214
  Angle     :  0.776   6.577   4464  Z= 0.412
  Chirality :  0.048   0.223    487
  Planarity :  0.005   0.043    565
  Dihedral  :  6.602  36.128    510
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 13.08 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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 (0.43), residues: 395
  helix: -3.01 (1.23), residues: 14
  sheet:  0.20 (0.50), residues: 130
  loop : -0.70 (0.38), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP H  47 
 PHE   0.025   0.003   PHE L  71 
 TYR   0.020   0.002   TYR C 489 
 ARG   0.006   0.001   ARG C 403 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00221 (    2)
  link_NAG-ASN         : angle       2.95864 (    6)
  link_BETA1-4         : bond        0.00432 (    1)
  link_BETA1-4         : angle       1.23866 (    3)
  hydrogen bonds       : bond        0.03760 (  104)
  hydrogen bonds       : angle       6.81695 (  249)
  SS BOND              : bond        0.00323 (    6)
  SS BOND              : angle       1.86456 (   12)
  covalent geometry    : bond        0.00470 ( 3275)
  covalent geometry    : angle       0.76316 ( 4443)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  353 TRP cc_start: 0.6478 (m-90) cc_final: 0.6205 (m-90)
REVERT: C  387 LEU cc_start: 0.8190 (tp) cc_final: 0.7702 (tp)
  outliers start: 12
  outliers final: 7
  residues processed: 58
  average time/residue: 0.1639
  time to fit residues: 11.5898
Evaluate side-chains
  51 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain C residue  351 TYR
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  503 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
H   1 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.075395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.068889 restraints weight = 14724.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.070477 restraints weight = 8000.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.071481 restraints weight = 4888.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.5482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   3284  Z= 0.277
  Angle     :  0.809   6.596   4464  Z= 0.429
  Chirality :  0.048   0.136    487
  Planarity :  0.005   0.046    565
  Dihedral  :  7.820  42.136    510
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 15.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 13.66 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -1.31 (0.42), residues: 395
  helix: -3.03 (1.29), residues: 14
  sheet: -0.30 (0.48), residues: 133
  loop : -1.07 (0.38), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP H  47 
 PHE   0.019   0.003   PHE C 338 
 TYR   0.017   0.002   TYR C 365 
 ARG   0.003   0.001   ARG C 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00136 (    2)
  link_NAG-ASN         : angle       2.87209 (    6)
  link_BETA1-4         : bond        0.00560 (    1)
  link_BETA1-4         : angle       1.03220 (    3)
  hydrogen bonds       : bond        0.04077 (  104)
  hydrogen bonds       : angle       7.07781 (  249)
  SS BOND              : bond        0.00460 (    6)
  SS BOND              : angle       0.78162 (   12)
  covalent geometry    : bond        0.00607 ( 3275)
  covalent geometry    : angle       0.80264 ( 4443)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  353 TRP cc_start: 0.6851 (m-90) cc_final: 0.6637 (m-90)
REVERT: C  382 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.7946 (m)
REVERT: C  387 LEU cc_start: 0.8242 (tp) cc_final: 0.7953 (tp)
  outliers start: 13
  outliers final: 7
  residues processed: 49
  average time/residue: 0.1617
  time to fit residues: 10.0617
Evaluate side-chains
  45 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain C residue  351 TYR
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  503 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0370
   chunk 1 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0060
   chunk 33 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.4274

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.078727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.072393 restraints weight = 14363.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.073951 restraints weight = 7688.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.074901 restraints weight = 4690.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.5652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3284  Z= 0.128
  Angle     :  0.656   5.894   4464  Z= 0.347
  Chirality :  0.046   0.133    487
  Planarity :  0.004   0.046    565
  Dihedral  :  6.490  36.644    510
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 15.12 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -1.19 (0.42), residues: 395
  helix: -3.24 (0.95), residues: 22
  sheet: -0.04 (0.49), residues: 127
  loop : -0.96 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP H  47 
 PHE   0.019   0.002   PHE L  71 
 TYR   0.011   0.001   TYR C 351 
 ARG   0.002   0.000   ARG C 509 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00062 (    2)
  link_NAG-ASN         : angle       2.54108 (    6)
  link_BETA1-4         : bond        0.00078 (    1)
  link_BETA1-4         : angle       1.27595 (    3)
  hydrogen bonds       : bond        0.03041 (  104)
  hydrogen bonds       : angle       6.38032 (  249)
  SS BOND              : bond        0.00250 (    6)
  SS BOND              : angle       0.75959 (   12)
  covalent geometry    : bond        0.00282 ( 3275)
  covalent geometry    : angle       0.64834 ( 4443)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   74 THR cc_start: 0.4216 (OUTLIER) cc_final: 0.3859 (p)
REVERT: C  387 LEU cc_start: 0.8374 (tp) cc_final: 0.8034 (tp)
  outliers start: 10
  outliers final: 8
  residues processed: 54
  average time/residue: 0.1738
  time to fit residues: 11.3035
Evaluate side-chains
  52 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   62 PHE
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain C residue  347 PHE
Chi-restraints excluded: chain C residue  351 TYR
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  503 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 7 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** L  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  38 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 = 0.3710 r_free = 0.3710 target = 0.077772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.071214 restraints weight = 14621.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.072784 restraints weight = 7679.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.073780 restraints weight = 4650.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.6047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3284  Z= 0.181
  Angle     :  0.676   5.891   4464  Z= 0.358
  Chirality :  0.045   0.139    487
  Planarity :  0.004   0.047    565
  Dihedral  :  6.713  38.413    510
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 14.24 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -1.36 (0.43), residues: 395
  helix: -3.35 (0.90), residues: 22
  sheet: -0.39 (0.48), residues: 134
  loop : -0.94 (0.40), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP C 353 
 PHE   0.012   0.002   PHE C 338 
 TYR   0.027   0.002   TYR L  92 
 ARG   0.008   0.001   ARG C 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00237 (    2)
  link_NAG-ASN         : angle       2.47365 (    6)
  link_BETA1-4         : bond        0.00140 (    1)
  link_BETA1-4         : angle       1.16723 (    3)
  hydrogen bonds       : bond        0.03142 (  104)
  hydrogen bonds       : angle       6.45728 (  249)
  SS BOND              : bond        0.00328 (    6)
  SS BOND              : angle       0.67994 (   12)
  covalent geometry    : bond        0.00399 ( 3275)
  covalent geometry    : angle       0.66953 ( 4443)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 45
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   74 THR cc_start: 0.4325 (OUTLIER) cc_final: 0.3895 (p)
REVERT: C  365 TYR cc_start: 0.5890 (m-80) cc_final: 0.5659 (m-80)
REVERT: C  387 LEU cc_start: 0.8337 (tp) cc_final: 0.8050 (tp)
REVERT: C  418 ILE cc_start: 0.9379 (mm) cc_final: 0.9161 (tp)
  outliers start: 13
  outliers final: 9
  residues processed: 52
  average time/residue: 0.1560
  time to fit residues: 9.9356
Evaluate side-chains
  49 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain C residue  351 TYR
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  503 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:    0.0870
   chunk 35 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0170
   chunk 13 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.4196

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.079146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.072632 restraints weight = 14058.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.074222 restraints weight = 7411.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.075230 restraints weight = 4489.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.6245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3284  Z= 0.128
  Angle     :  0.635   6.308   4464  Z= 0.335
  Chirality :  0.045   0.139    487
  Planarity :  0.005   0.045    565
  Dihedral  :  6.279  37.043    510
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 15.12 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -1.19 (0.43), residues: 395
  helix: -3.28 (0.94), residues: 22
  sheet: -0.17 (0.49), residues: 129
  loop : -0.88 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.003   TRP C 353 
 PHE   0.009   0.001   PHE C 429 
 TYR   0.017   0.001   TYR L  92 
 ARG   0.006   0.000   ARG C 466 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00113 (    2)
  link_NAG-ASN         : angle       2.42554 (    6)
  link_BETA1-4         : bond        0.00117 (    1)
  link_BETA1-4         : angle       1.21183 (    3)
  hydrogen bonds       : bond        0.02845 (  104)
  hydrogen bonds       : angle       6.27788 (  249)
  SS BOND              : bond        0.00216 (    6)
  SS BOND              : angle       0.63707 (   12)
  covalent geometry    : bond        0.00282 ( 3275)
  covalent geometry    : angle       0.62879 ( 4443)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   74 THR cc_start: 0.4268 (OUTLIER) cc_final: 0.3928 (p)
REVERT: L  103 LYS cc_start: 0.7571 (tptp) cc_final: 0.7357 (tppt)
REVERT: C  365 TYR cc_start: 0.5823 (m-80) cc_final: 0.5616 (m-80)
REVERT: C  387 LEU cc_start: 0.8227 (tp) cc_final: 0.7940 (tp)
REVERT: C  418 ILE cc_start: 0.9390 (mm) cc_final: 0.9177 (tp)
  outliers start: 11
  outliers final: 10
  residues processed: 51
  average time/residue: 0.1696
  time to fit residues: 10.7034
Evaluate side-chains
  52 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   62 PHE
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain C residue  347 PHE
Chi-restraints excluded: chain C residue  351 TYR
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  503 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 5 optimal weight:    0.1980
   chunk 30 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0980
   chunk 6 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 24 optimal weight:    0.4980
   chunk 35 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
L  27 GLN
** L  38 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 = 0.3735 r_free = 0.3735 target = 0.078973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.072580 restraints weight = 14103.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.074108 restraints weight = 7506.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.075077 restraints weight = 4578.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.6530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3284  Z= 0.127
  Angle     :  0.607   5.876   4464  Z= 0.320
  Chirality :  0.044   0.138    487
  Planarity :  0.004   0.046    565
  Dihedral  :  5.997  35.955    510
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 14.83 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -1.13 (0.43), residues: 395
  helix: -3.60 (0.73), residues: 28
  sheet:  0.21 (0.51), residues: 120
  loop : -0.90 (0.40), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 353 
 PHE   0.009   0.001   PHE C 429 
 TYR   0.015   0.001   TYR C 351 
 ARG   0.002   0.000   ARG C 509 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00203 (    2)
  link_NAG-ASN         : angle       2.25734 (    6)
  link_BETA1-4         : bond        0.00125 (    1)
  link_BETA1-4         : angle       1.21571 (    3)
  hydrogen bonds       : bond        0.02688 (  104)
  hydrogen bonds       : angle       5.99755 (  249)
  SS BOND              : bond        0.00207 (    6)
  SS BOND              : angle       0.74456 (   12)
  covalent geometry    : bond        0.00281 ( 3275)
  covalent geometry    : angle       0.60092 ( 4443)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   74 THR cc_start: 0.4178 (OUTLIER) cc_final: 0.3889 (p)
REVERT: L  103 LYS cc_start: 0.7529 (tptp) cc_final: 0.7143 (tppt)
REVERT: C  347 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7853 (t80)
REVERT: C  468 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8534 (tp)
  outliers start: 14
  outliers final: 11
  residues processed: 54
  average time/residue: 0.1423
  time to fit residues: 9.5975
Evaluate side-chains
  52 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 38
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   82 ASP
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain C residue  347 PHE
Chi-restraints excluded: chain C residue  351 TYR
Chi-restraints excluded: chain C residue  353 TRP
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  503 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0770
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.6338

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.078307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.071997 restraints weight = 14463.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.073509 restraints weight = 7588.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.074447 restraints weight = 4584.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.6631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3284  Z= 0.146
  Angle     :  0.652   8.778   4464  Z= 0.340
  Chirality :  0.046   0.135    487
  Planarity :  0.004   0.045    565
  Dihedral  :  6.172  36.961    510
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.73 %
    Favored  : 79.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -1.18 (0.42), residues: 395
  helix: -3.45 (0.76), residues: 28
  sheet:  0.56 (0.53), residues: 106
  loop : -1.10 (0.38), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H  47 
 PHE   0.009   0.001   PHE C 338 
 TYR   0.016   0.001   TYR C 351 
 ARG   0.007   0.000   ARG C 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00134 (    2)
  link_NAG-ASN         : angle       2.29471 (    6)
  link_BETA1-4         : bond        0.00161 (    1)
  link_BETA1-4         : angle       1.14099 (    3)
  hydrogen bonds       : bond        0.02904 (  104)
  hydrogen bonds       : angle       6.19171 (  249)
  SS BOND              : bond        0.00218 (    6)
  SS BOND              : angle       0.70534 (   12)
  covalent geometry    : bond        0.00325 ( 3275)
  covalent geometry    : angle       0.64647 ( 4443)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   74 THR cc_start: 0.4235 (OUTLIER) cc_final: 0.3944 (p)
REVERT: C  347 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7803 (t80)
REVERT: C  396 TYR cc_start: 0.6810 (m-80) cc_final: 0.6455 (m-80)
  outliers start: 11
  outliers final: 9
  residues processed: 46
  average time/residue: 0.1687
  time to fit residues: 9.5161
Evaluate side-chains
  48 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 37
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain C residue  347 PHE
Chi-restraints excluded: chain C residue  351 TYR
Chi-restraints excluded: chain C residue  353 TRP
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  503 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 23 optimal weight:    0.3980
   chunk 4 optimal weight:    2.9990
   chunk 35 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** L  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 481 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.078061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.071700 restraints weight = 14252.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.073195 restraints weight = 7532.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.074089 restraints weight = 4571.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.6741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3284  Z= 0.153
  Angle     :  0.666   8.651   4464  Z= 0.346
  Chirality :  0.046   0.136    487
  Planarity :  0.004   0.045    565
  Dihedral  :  6.243  37.529    510
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.73 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -1.30 (0.42), residues: 395
  helix: -3.61 (0.64), residues: 34
  sheet:  0.36 (0.51), residues: 112
  loop : -1.06 (0.39), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP H  47 
 PHE   0.009   0.001   PHE C 338 
 TYR   0.015   0.001   TYR C 351 
 ARG   0.002   0.000   ARG C 509 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00185 (    2)
  link_NAG-ASN         : angle       2.27628 (    6)
  link_BETA1-4         : bond        0.00287 (    1)
  link_BETA1-4         : angle       1.13341 (    3)
  hydrogen bonds       : bond        0.02916 (  104)
  hydrogen bonds       : angle       6.16464 (  249)
  SS BOND              : bond        0.00264 (    6)
  SS BOND              : angle       0.78236 (   12)
  covalent geometry    : bond        0.00342 ( 3275)
  covalent geometry    : angle       0.66039 ( 4443)

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

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

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  790 Ramachandran restraints generated.
    395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 39
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   74 THR cc_start: 0.4173 (OUTLIER) cc_final: 0.3835 (p)
REVERT: C  347 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7785 (t80)
REVERT: C  396 TYR cc_start: 0.6859 (m-80) cc_final: 0.6374 (m-80)
  outliers start: 12
  outliers final: 8
  residues processed: 47
  average time/residue: 0.1633
  time to fit residues: 9.6209
Evaluate side-chains
  46 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 36
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue  104 VAL
Chi-restraints excluded: chain C residue  347 PHE
Chi-restraints excluded: chain C residue  353 TRP
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  503 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0970
   chunk 38 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.5978

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.078135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.071695 restraints weight = 14340.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.073198 restraints weight = 7612.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.074131 restraints weight = 4627.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.6842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3284  Z= 0.146
  Angle     :  0.672   8.254   4464  Z= 0.351
  Chirality :  0.047   0.147    487
  Planarity :  0.004   0.044    565
  Dihedral  :  6.188  37.543    510
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.85 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.73 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    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: -1.32 (0.42), residues: 395
  helix: -3.59 (0.65), residues: 34
  sheet:  0.49 (0.52), residues: 106
  loop : -1.12 (0.39), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP H  47 
 PHE   0.008   0.001   PHE C 429 
 TYR   0.012   0.001   TYR L  92 
 ARG   0.002   0.000   ARG C 509 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00146 (    2)
  link_NAG-ASN         : angle       2.25269 (    6)
  link_BETA1-4         : bond        0.00062 (    1)
  link_BETA1-4         : angle       1.17687 (    3)
  hydrogen bonds       : bond        0.02810 (  104)
  hydrogen bonds       : angle       6.05523 (  249)
  SS BOND              : bond        0.00266 (    6)
  SS BOND              : angle       0.72565 (   12)
  covalent geometry    : bond        0.00325 ( 3275)
  covalent geometry    : angle       0.66658 ( 4443)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1811.92 seconds
wall clock time: 32 minutes 52.16 seconds (1972.16 seconds total)