Starting phenix.real_space_refine
on Wed Jul 23 13:27:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jva_22497/07_2025/7jva_22497.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jva_22497/07_2025/7jva_22497.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jva_22497/07_2025/7jva_22497.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jva_22497/07_2025/7jva_22497.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jva_22497/07_2025/7jva_22497.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jva_22497/07_2025/7jva_22497.cif"
  }
  resolution = 3.6
  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=   0.000 sd=   0.021
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    2068      2.51       5
     N     548      2.21       5
     O     617      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 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: 3248
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 911
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 911
          Classifications: {'peptide': 117}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 2, 'TRANS': 114}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "L"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 803
          Classifications: {'peptide': 110}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 6, 'TRANS': 103}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "A"
      Number of atoms: 1495
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1495
          Classifications: {'peptide': 193}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 11, 'TRANS': 181}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 3.35, per 1000 atoms: 1.03
  Number of scatterers: 3248
  At special positions: 0
  Unit cell: (89.25, 75.6, 70.35, 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     617      8.00
     N     548      7.00
     C    2068      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  96 " distance=2.09
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  91 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.07

  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 B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
    NAG-ASN
      " NAG B   1 " - " ASN A 343 "
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 365.4 milliseconds
  

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  766

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 10 sheets defined
      13.3% alpha, 35.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 62 through 65
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'L' and resid 28 through 32
      removed outlier: 4.028A  pdb=" N   ASN L  32 " --> pdb=" O   ILE L  29 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 69 through 71
      No H-bonds generated for 'chain 'L' and resid 69 through 71'
    Processing helix  chain 'A' and resid 337 through 343
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 386 through 390
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.358A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11
      removed outlier: 6.815A  pdb=" N   MET H  34 " --> pdb=" O   ASN H  50 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   ASN H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11
      removed outlier: 3.922A  pdb=" N   TYR H 108 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11
      removed outlier: 5.951A  pdb=" N   GLN L  38 " --> pdb=" O   THR L  47 " (cutoff:3.500A)
      removed outlier: 5.747A  pdb=" N   THR L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 11
    Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23
    Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.530A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474

    129 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: 1.12

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 586
        1.31 -     1.45: 1042
        1.45 -     1.58: 1682
        1.58 -     1.71: 4
        1.71 -     1.84: 18
  Bond restraints: 3332
  Sorted by residual:
  bond pdb=" CD  GLU H   6 "
       pdb=" OE2 GLU H   6 "
    ideal  model  delta    sigma   weight residual
    1.249  1.182  0.067 1.90e-02 2.77e+03 1.23e+01
  bond pdb=" CB  ASN A 422 "
       pdb=" CG  ASN A 422 "
    ideal  model  delta    sigma   weight residual
    1.516  1.437  0.079 2.50e-02 1.60e+03 9.92e+00
  bond pdb=" CB  ASN H  50 "
       pdb=" CG  ASN H  50 "
    ideal  model  delta    sigma   weight residual
    1.516  1.437  0.079 2.50e-02 1.60e+03 9.89e+00
  bond pdb=" C5  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.476 -0.063 2.00e-02 2.50e+03 9.85e+00
  bond pdb=" NE  ARG A 357 "
       pdb=" CZ  ARG A 357 "
    ideal  model  delta    sigma   weight residual
    1.326  1.360 -0.034 1.10e-02 8.26e+03 9.59e+00
  ... (remaining 3327 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.15: 4438
        4.15 -     8.30: 98
        8.30 -    12.45: 1
       12.45 -    16.60: 0
       16.60 -    20.75: 2
  Bond angle restraints: 4539
  Sorted by residual:
  angle pdb=" CD1 LEU H  86 "
        pdb=" CG  LEU H  86 "
        pdb=" CD2 LEU H  86 "
      ideal   model   delta    sigma   weight residual
     110.80  131.55  -20.75 2.20e+00 2.07e-01 8.89e+01
  angle pdb=" CG1 VAL H   2 "
        pdb=" CB  VAL H   2 "
        pdb=" CG2 VAL H   2 "
      ideal   model   delta    sigma   weight residual
     110.80  131.11  -20.31 2.20e+00 2.07e-01 8.52e+01
  angle pdb=" C   SER A 383 "
        pdb=" N   PRO A 384 "
        pdb=" CA  PRO A 384 "
      ideal   model   delta    sigma   weight residual
     119.56  127.19   -7.63 1.02e+00 9.61e-01 5.60e+01
  angle pdb=" C   LEU A 425 "
        pdb=" N   PRO A 426 "
        pdb=" CA  PRO A 426 "
      ideal   model   delta    sigma   weight residual
     119.85  126.34   -6.49 1.01e+00 9.80e-01 4.12e+01
  angle pdb=" C   GLN A 498 "
        pdb=" N   PRO A 499 "
        pdb=" CA  PRO A 499 "
      ideal   model   delta    sigma   weight residual
     119.56  126.05   -6.49 1.02e+00 9.61e-01 4.04e+01
  ... (remaining 4534 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.24: 1898
       21.24 -    42.49: 57
       42.49 -    63.73: 8
       63.73 -    84.98: 8
       84.98 -   106.22: 5
  Dihedral angle restraints: 1976
    sinusoidal: 767
      harmonic: 1209
  Sorted by residual:
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -36.13  -49.87     1      1.00e+01 1.00e-02 3.41e+01
  dihedral pdb=" O4  BMA B   3 "
           pdb=" C4  BMA B   3 "
           pdb=" C5  BMA B   3 "
           pdb=" O5  BMA B   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -177.51  106.22     1      3.00e+01 1.11e-03 1.36e+01
  dihedral pdb=" C3  BMA B   3 "
           pdb=" C4  BMA B   3 "
           pdb=" C5  BMA B   3 "
           pdb=" O5  BMA B   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.62  -57.96  105.58     1      3.00e+01 1.11e-03 1.35e+01
  ... (remaining 1973 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 422
       0.112 -    0.224: 60
       0.224 -    0.336: 9
       0.336 -    0.448: 3
       0.448 -    0.560: 2
  Chirality restraints: 496
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.62    0.22 2.00e-02 2.50e+03 1.25e+02
  chirality pdb=" C1  BMA B   3 "
            pdb=" O4  NAG B   2 "
            pdb=" C2  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.48    0.08 2.00e-02 2.50e+03 1.68e+01
  chirality pdb=" CG  LEU H  86 "
            pdb=" CB  LEU H  86 "
            pdb=" CD1 LEU H  86 "
            pdb=" CD2 LEU H  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.03   -0.56 2.00e-01 2.50e+01 7.83e+00
  ... (remaining 493 not shown)

  Planarity restraints: 586
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H 108 "    0.036 2.00e-02 2.50e+03   1.86e-02 6.92e+00
        pdb=" CG  TYR H 108 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD1 TYR H 108 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR H 108 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 TYR H 108 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR H 108 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR H 108 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR H 108 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 495 "   -0.035 2.00e-02 2.50e+03   1.83e-02 6.70e+00
        pdb=" CG  TYR A 495 "    0.013 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 495 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 495 "    0.016 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 495 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 495 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 495 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 495 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  37 "    0.027 2.00e-02 2.50e+03   1.51e-02 4.59e+00
        pdb=" CG  TYR L  37 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  37 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  37 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  37 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  37 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  37 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR L  37 "    0.024 2.00e-02 2.50e+03
  ... (remaining 583 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 1320
        2.90 -     3.40: 2801
        3.40 -     3.90: 5451
        3.90 -     4.40: 6366
        4.40 -     4.90: 10508
  Nonbonded interactions: 26446
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP L  52 "
            pdb=" NZ  LYS A 378 "
     model   vdw
     2.398 3.120
  nonbonded pdb=" OE2 GLU H   6 "
            pdb=" N   GLN H 111 "
     model   vdw
     2.536 3.120
  nonbonded pdb=" N   ASN A 440 "
            pdb=" OD1 ASN A 440 "
     model   vdw
     2.551 3.120
  nonbonded pdb=" N   ASP A 428 "
            pdb=" OD1 ASP A 428 "
     model   vdw
     2.552 3.120
  nonbonded pdb=" N   CYS H  96 "
            pdb=" O   CYS H  96 "
     model   vdw
     2.557 2.496
  ... (remaining 26441 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     14.110
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:4.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
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      :  0.016   0.079   3341  Z= 0.861
  Angle     :  1.533  20.747   4560  Z= 0.985
  Chirality :  0.093   0.560    496
  Planarity :  0.006   0.034    585
  Dihedral  : 13.100 106.220   1192
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 0.80
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  0.97 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  1.22 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.87 (0.43), residues: 412
  helix: -4.22 (0.39), residues: 28
  sheet:  0.47 (0.42), residues: 154
  loop :  1.57 (0.44), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.007   TRP H  33 
 HIS   0.002   0.001   HIS L   8 
 PHE   0.024   0.004   PHE H  29 
 TYR   0.036   0.006   TYR H 108 
 ARG   0.007   0.001   ARG H  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.05556 (    1)
  link_NAG-ASN         : angle       2.05395 (    3)
  link_BETA1-4         : bond        0.07331 (    2)
  link_BETA1-4         : angle       4.68704 (    6)
  hydrogen bonds       : bond        0.19354 (  117)
  hydrogen bonds       : angle       8.62319 (  285)
  SS BOND              : bond        0.02855 (    6)
  SS BOND              : angle       3.67329 (   12)
  covalent geometry    : bond        0.01578 ( 3332)
  covalent geometry    : angle       1.51478 ( 4539)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   91 THR cc_start: 0.8640 (m) cc_final: 0.8342 (t)
REVERT: L   37 TYR cc_start: 0.9058 (m-80) cc_final: 0.8676 (m-10)
REVERT: A  375 SER cc_start: 0.8854 (m) cc_final: 0.8575 (t)
  outliers start: 1
  outliers final: 1
  residues processed: 100
  average time/residue: 0.2104
  time to fit residues: 24.3890
Evaluate side-chains
  64 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   86 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.3980
   chunk 31 optimal weight:    0.3980
   chunk 17 optimal weight:    0.7980
   chunk 10 optimal weight:    0.2980
   chunk 20 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 23 optimal weight:    0.1980
   chunk 37 optimal weight:    0.0870
   overall best weight:    0.2758

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

Flipped N/Q/H residues before XYZ refinement:
L  38 GLN
L  99 HIS
A 394 ASN
A 506 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.124329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.113634 restraints weight = 5667.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.116639 restraints weight = 2894.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.118570 restraints weight = 1755.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3341  Z= 0.171
  Angle     :  0.708   9.033   4560  Z= 0.362
  Chirality :  0.048   0.171    496
  Planarity :  0.004   0.033    585
  Dihedral  :  9.557  64.465    525
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  0.49 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 10.67 %
    Favored  : 86.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.42), residues: 412
  helix: -3.47 (0.68), residues: 28
  sheet:  0.57 (0.42), residues: 150
  loop :  1.21 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP H  33 
 HIS   0.003   0.001   HIS L  99 
 PHE   0.012   0.002   PHE H 106 
 TYR   0.022   0.002   TYR H  32 
 ARG   0.004   0.001   ARG L  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00644 (    1)
  link_NAG-ASN         : angle       4.02769 (    3)
  link_BETA1-4         : bond        0.00907 (    2)
  link_BETA1-4         : angle       4.36163 (    6)
  hydrogen bonds       : bond        0.04721 (  117)
  hydrogen bonds       : angle       6.97519 (  285)
  SS BOND              : bond        0.00328 (    6)
  SS BOND              : angle       1.58223 (   12)
  covalent geometry    : bond        0.00374 ( 3332)
  covalent geometry    : angle       0.67880 ( 4539)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   12 VAL cc_start: 0.6312 (OUTLIER) cc_final: 0.6036 (m)
REVERT: H   60 TYR cc_start: 0.9005 (m-80) cc_final: 0.8802 (m-80)
REVERT: H   91 THR cc_start: 0.8596 (m) cc_final: 0.8394 (t)
REVERT: L   37 TYR cc_start: 0.9013 (m-80) cc_final: 0.8801 (m-10)
REVERT: A  375 SER cc_start: 0.8884 (m) cc_final: 0.8546 (t)
  outliers start: 9
  outliers final: 8
  residues processed: 78
  average time/residue: 0.1526
  time to fit residues: 14.8769
Evaluate side-chains
  76 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   91 CYS
Chi-restraints excluded: chain L residue  109 THR
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  443 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0980
   chunk 23 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0050
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.119967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.108853 restraints weight = 5706.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.111802 restraints weight = 3003.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.113754 restraints weight = 1883.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   3341  Z= 0.228
  Angle     :  0.725  10.758   4560  Z= 0.362
  Chirality :  0.047   0.163    496
  Planarity :  0.005   0.040    585
  Dihedral  :  7.371  39.572    523
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 10.06 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.38 (0.42), residues: 412
  helix: -3.39 (0.71), residues: 28
  sheet:  0.28 (0.44), residues: 141
  loop :  0.90 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP H  33 
 HIS   0.004   0.002   HIS L  99 
 PHE   0.012   0.002   PHE H 106 
 TYR   0.016   0.002   TYR A 495 
 ARG   0.004   0.001   ARG H  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00722 (    1)
  link_NAG-ASN         : angle       2.58339 (    3)
  link_BETA1-4         : bond        0.01001 (    2)
  link_BETA1-4         : angle       3.91873 (    6)
  hydrogen bonds       : bond        0.04434 (  117)
  hydrogen bonds       : angle       6.65356 (  285)
  SS BOND              : bond        0.00449 (    6)
  SS BOND              : angle       1.31733 (   12)
  covalent geometry    : bond        0.00514 ( 3332)
  covalent geometry    : angle       0.70597 ( 4539)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 1.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   55 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7948 (ptt-90)
REVERT: A  375 SER cc_start: 0.8912 (m) cc_final: 0.8551 (t)
REVERT: A  441 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8280 (mp)
REVERT: A  506 GLN cc_start: 0.8289 (mp10) cc_final: 0.7785 (mp10)
  outliers start: 15
  outliers final: 8
  residues processed: 77
  average time/residue: 0.1821
  time to fit residues: 17.3579
Evaluate side-chains
  73 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   86 GLU
Chi-restraints excluded: chain L residue   91 CYS
Chi-restraints excluded: chain L residue  109 THR
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  443 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 25 optimal weight:    0.2980
   chunk 40 optimal weight:    0.1980
   chunk 24 optimal weight:    0.2980
   chunk 16 optimal weight:    0.0770
   chunk 5 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0870
   overall best weight:    0.1916

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN

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 = 0.122399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.111373 restraints weight = 5773.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.114381 restraints weight = 3013.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.116329 restraints weight = 1852.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3341  Z= 0.130
  Angle     :  0.643  10.746   4560  Z= 0.319
  Chirality :  0.046   0.146    496
  Planarity :  0.004   0.054    585
  Dihedral  :  6.035  34.413    523
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 10.98 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.44 (0.42), residues: 412
  helix: -3.24 (0.77), residues: 28
  sheet:  0.27 (0.42), residues: 149
  loop :  0.98 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  33 
 HIS   0.003   0.001   HIS L  99 
 PHE   0.013   0.001   PHE H  68 
 TYR   0.012   0.001   TYR A 369 
 ARG   0.006   0.001   ARG L  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00601 (    1)
  link_NAG-ASN         : angle       1.83453 (    3)
  link_BETA1-4         : bond        0.00916 (    2)
  link_BETA1-4         : angle       3.52871 (    6)
  hydrogen bonds       : bond        0.03876 (  117)
  hydrogen bonds       : angle       6.38576 (  285)
  SS BOND              : bond        0.00528 (    6)
  SS BOND              : angle       1.29831 (   12)
  covalent geometry    : bond        0.00291 ( 3332)
  covalent geometry    : angle       0.62584 ( 4539)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   55 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7845 (ptt-90)
REVERT: L  109 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8383 (p)
REVERT: A  375 SER cc_start: 0.8907 (m) cc_final: 0.8551 (t)
REVERT: A  441 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8279 (mp)
REVERT: A  506 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7995 (mp10)
  outliers start: 12
  outliers final: 7
  residues processed: 77
  average time/residue: 0.1595
  time to fit residues: 15.2740
Evaluate side-chains
  73 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   52 ASP
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   86 GLU
Chi-restraints excluded: chain L residue   91 CYS
Chi-restraints excluded: chain L residue  109 THR
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  506 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    0.0970
   chunk 28 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0980
   chunk 24 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 1 optimal weight:    0.4980
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.120630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.109504 restraints weight = 5824.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.112431 restraints weight = 3071.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.114324 restraints weight = 1918.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3341  Z= 0.187
  Angle     :  0.667  10.656   4560  Z= 0.332
  Chirality :  0.046   0.159    496
  Planarity :  0.004   0.051    585
  Dihedral  :  5.706  33.104    523
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 11.28 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.38 (0.42), residues: 412
  helix: -2.67 (1.01), residues: 21
  sheet:  0.15 (0.44), residues: 148
  loop :  0.78 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  36 
 HIS   0.003   0.002   HIS L  99 
 PHE   0.011   0.001   PHE A 456 
 TYR   0.013   0.001   TYR A 495 
 ARG   0.009   0.001   ARG L  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00619 (    1)
  link_NAG-ASN         : angle       1.79034 (    3)
  link_BETA1-4         : bond        0.00917 (    2)
  link_BETA1-4         : angle       3.25139 (    6)
  hydrogen bonds       : bond        0.03895 (  117)
  hydrogen bonds       : angle       6.26773 (  285)
  SS BOND              : bond        0.00311 (    6)
  SS BOND              : angle       1.18026 (   12)
  covalent geometry    : bond        0.00418 ( 3332)
  covalent geometry    : angle       0.65396 ( 4539)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 1.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   72 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8088 (ttp80)
REVERT: H   98 ARG cc_start: 0.7850 (ttp-170) cc_final: 0.7554 (ttp-170)
REVERT: L   55 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7870 (ptt-90)
REVERT: L  109 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8491 (p)
REVERT: A  375 SER cc_start: 0.8928 (m) cc_final: 0.8603 (t)
REVERT: A  441 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8352 (mp)
REVERT: A  506 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8063 (mp10)
  outliers start: 17
  outliers final: 8
  residues processed: 82
  average time/residue: 0.3622
  time to fit residues: 36.7061
Evaluate side-chains
  82 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   72 ARG
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   52 ASP
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   76 LEU
Chi-restraints excluded: chain L residue   86 GLU
Chi-restraints excluded: chain L residue  109 THR
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  506 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0870
   chunk 17 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 11 optimal weight:    0.3980
   chunk 21 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0970
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.3756

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.120339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.108973 restraints weight = 5958.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.111941 restraints weight = 3143.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.113869 restraints weight = 1966.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.3746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3341  Z= 0.179
  Angle     :  0.667  10.961   4560  Z= 0.332
  Chirality :  0.046   0.159    496
  Planarity :  0.004   0.048    585
  Dihedral  :  5.555  34.020    523
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 14.02 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.25 (0.42), residues: 412
  helix: -2.59 (1.02), residues: 21
  sheet: -0.07 (0.43), residues: 148
  loop :  0.78 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H 101 
 HIS   0.003   0.002   HIS L  99 
 PHE   0.011   0.001   PHE A 456 
 TYR   0.012   0.001   TYR A 369 
 ARG   0.007   0.001   ARG L  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00567 (    1)
  link_NAG-ASN         : angle       1.72324 (    3)
  link_BETA1-4         : bond        0.00814 (    2)
  link_BETA1-4         : angle       3.02071 (    6)
  hydrogen bonds       : bond        0.03826 (  117)
  hydrogen bonds       : angle       6.30084 (  285)
  SS BOND              : bond        0.00272 (    6)
  SS BOND              : angle       1.42442 (   12)
  covalent geometry    : bond        0.00402 ( 3332)
  covalent geometry    : angle       0.65427 ( 4539)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   55 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7917 (ptt-90)
REVERT: L  109 THR cc_start: 0.8846 (m) cc_final: 0.8542 (p)
REVERT: A  506 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8089 (mp10)
  outliers start: 12
  outliers final: 8
  residues processed: 78
  average time/residue: 0.2224
  time to fit residues: 21.4738
Evaluate side-chains
  77 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   52 ASP
Chi-restraints excluded: chain L residue   55 ARG
Chi-restraints excluded: chain L residue   76 LEU
Chi-restraints excluded: chain L residue   86 GLU
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  506 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    0.4980
   chunk 7 optimal weight:    0.0980
   chunk 9 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 36 optimal weight:    0.0970
   chunk 28 optimal weight:    0.3980
   chunk 8 optimal weight:    0.0470
   chunk 5 optimal weight:    0.0470
   chunk 29 optimal weight:    0.0050
   overall best weight:    0.0588

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.124080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.113122 restraints weight = 5760.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.116025 restraints weight = 3018.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.117898 restraints weight = 1879.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.3883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   3341  Z= 0.112
  Angle     :  0.628  10.692   4560  Z= 0.312
  Chirality :  0.044   0.138    496
  Planarity :  0.004   0.047    585
  Dihedral  :  5.243  32.980    523
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.16 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.44 (0.42), residues: 412
  helix: -2.43 (1.07), residues: 21
  sheet: -0.02 (0.44), residues: 144
  loop :  0.96 (0.41), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.001   0.001   HIS L  99 
 PHE   0.010   0.001   PHE A 456 
 TYR   0.009   0.001   TYR A 369 
 ARG   0.007   0.000   ARG L  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00488 (    1)
  link_NAG-ASN         : angle       1.42396 (    3)
  link_BETA1-4         : bond        0.01075 (    2)
  link_BETA1-4         : angle       2.85792 (    6)
  hydrogen bonds       : bond        0.03470 (  117)
  hydrogen bonds       : angle       6.16409 (  285)
  SS BOND              : bond        0.00261 (    6)
  SS BOND              : angle       1.12047 (   12)
  covalent geometry    : bond        0.00248 ( 3332)
  covalent geometry    : angle       0.61693 ( 4539)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   59 TYR cc_start: 0.8113 (m-10) cc_final: 0.7885 (m-10)
REVERT: L  109 THR cc_start: 0.8851 (m) cc_final: 0.8628 (p)
REVERT: A  506 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8110 (mp10)
  outliers start: 8
  outliers final: 3
  residues processed: 81
  average time/residue: 0.1516
  time to fit residues: 15.0524
Evaluate side-chains
  74 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 ASP
Chi-restraints excluded: chain L residue   76 LEU
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  506 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0870
   chunk 8 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0170
   chunk 1 optimal weight:    0.0870
   chunk 13 optimal weight:    0.0980
   chunk 40 optimal weight:    0.4980
   chunk 10 optimal weight:    0.7980
   chunk 9 optimal weight:    0.1980
   overall best weight:    0.0974

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.124434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.113467 restraints weight = 5768.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.116376 restraints weight = 3024.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.118233 restraints weight = 1881.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.4107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3341  Z= 0.115
  Angle     :  0.642   9.959   4560  Z= 0.319
  Chirality :  0.044   0.169    496
  Planarity :  0.004   0.051    585
  Dihedral  :  5.162  31.900    523
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 16.16 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.51 (0.43), residues: 412
  helix: -2.15 (1.16), residues: 21
  sheet: -0.05 (0.44), residues: 144
  loop :  1.03 (0.42), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 436 
 HIS   0.001   0.001   HIS L  99 
 PHE   0.009   0.001   PHE A 456 
 TYR   0.018   0.001   TYR A 508 
 ARG   0.007   0.000   ARG L  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00465 (    1)
  link_NAG-ASN         : angle       1.37212 (    3)
  link_BETA1-4         : bond        0.00791 (    2)
  link_BETA1-4         : angle       2.82919 (    6)
  hydrogen bonds       : bond        0.03381 (  117)
  hydrogen bonds       : angle       6.11828 (  285)
  SS BOND              : bond        0.00256 (    6)
  SS BOND              : angle       1.09938 (   12)
  covalent geometry    : bond        0.00261 ( 3332)
  covalent geometry    : angle       0.63180 ( 4539)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  109 THR cc_start: 0.8815 (m) cc_final: 0.8525 (p)
REVERT: A  506 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8165 (mp10)
  outliers start: 9
  outliers final: 5
  residues processed: 79
  average time/residue: 0.1321
  time to fit residues: 13.1905
Evaluate side-chains
  76 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   52 ASP
Chi-restraints excluded: chain L residue   76 LEU
Chi-restraints excluded: chain A residue  394 ASN
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  506 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 35 optimal weight:    0.3980
   chunk 19 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 16 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0050
   chunk 21 optimal weight:    0.3980
   chunk 11 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0670
   overall best weight:    0.2732

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.114011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.104212 restraints weight = 5956.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.106594 restraints weight = 3410.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.108164 restraints weight = 2228.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.4187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3341  Z= 0.152
  Angle     :  0.674   9.761   4560  Z= 0.334
  Chirality :  0.045   0.186    496
  Planarity :  0.005   0.078    585
  Dihedral  :  5.200  31.995    523
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.68 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.58 (0.43), residues: 412
  helix: -2.55 (1.04), residues: 21
  sheet:  0.14 (0.44), residues: 148
  loop :  1.03 (0.42), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 101 
 HIS   0.003   0.001   HIS L  99 
 PHE   0.010   0.001   PHE A 456 
 TYR   0.010   0.001   TYR H  59 
 ARG   0.005   0.000   ARG L  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00475 (    1)
  link_NAG-ASN         : angle       1.49293 (    3)
  link_BETA1-4         : bond        0.00876 (    2)
  link_BETA1-4         : angle       2.78522 (    6)
  hydrogen bonds       : bond        0.03497 (  117)
  hydrogen bonds       : angle       6.14350 (  285)
  SS BOND              : bond        0.00253 (    6)
  SS BOND              : angle       1.21450 (   12)
  covalent geometry    : bond        0.00347 ( 3332)
  covalent geometry    : angle       0.66360 ( 4539)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L  109 THR cc_start: 0.8698 (m) cc_final: 0.8446 (p)
REVERT: A  506 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8199 (mp10)
  outliers start: 8
  outliers final: 6
  residues processed: 75
  average time/residue: 0.1393
  time to fit residues: 12.9564
Evaluate side-chains
  76 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain L residue   52 ASP
Chi-restraints excluded: chain L residue   76 LEU
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  506 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0770
   chunk 22 optimal weight:    0.8980
   chunk 13 optimal weight:    0.1980
   chunk 38 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0670
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0270
   overall best weight:    0.1934

-------------------------------------------------------------------------------
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 = 0.3572 r_free = 0.3572 target = 0.111748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.102307 restraints weight = 5839.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.104674 restraints weight = 3380.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.106222 restraints weight = 2214.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.4350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3341  Z= 0.131
  Angle     :  0.662   9.959   4560  Z= 0.328
  Chirality :  0.044   0.186    496
  Planarity :  0.004   0.038    585
  Dihedral  :  5.163  31.943    523
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 17.07 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.50 (0.43), residues: 412
  helix: -2.53 (1.04), residues: 21
  sheet:  0.02 (0.44), residues: 144
  loop :  1.01 (0.42), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  33 
 HIS   0.002   0.001   HIS L  99 
 PHE   0.009   0.001   PHE L  63 
 TYR   0.009   0.001   TYR H  59 
 ARG   0.003   0.000   ARG L  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00413 (    1)
  link_NAG-ASN         : angle       1.43265 (    3)
  link_BETA1-4         : bond        0.00838 (    2)
  link_BETA1-4         : angle       2.71892 (    6)
  hydrogen bonds       : bond        0.03404 (  117)
  hydrogen bonds       : angle       6.03900 (  285)
  SS BOND              : bond        0.00265 (    6)
  SS BOND              : angle       1.20416 (   12)
  covalent geometry    : bond        0.00300 ( 3332)
  covalent geometry    : angle       0.65231 ( 4539)

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

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

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  824 Ramachandran restraints generated.
    412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   11 LEU cc_start: 0.8484 (pp) cc_final: 0.8139 (pp)
  outliers start: 9
  outliers final: 8
  residues processed: 74
  average time/residue: 0.1519
  time to fit residues: 14.4933
Evaluate side-chains
  73 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   99 VAL
Chi-restraints excluded: chain L residue   52 ASP
Chi-restraints excluded: chain L residue   76 LEU
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  430 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 19 optimal weight:    0.4980
   chunk 7 optimal weight:    0.4980
   chunk 39 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0370
   chunk 3 optimal weight:    0.3980
   chunk 38 optimal weight:    0.6980
   chunk 28 optimal weight:    0.3980
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.3658

-------------------------------------------------------------------------------
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 = 0.3572 r_free = 0.3572 target = 0.112429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.102717 restraints weight = 5910.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.105055 restraints weight = 3410.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.106648 restraints weight = 2249.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.4437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.094   3341  Z= 0.184
  Angle     :  0.716  16.403   4560  Z= 0.347
  Chirality :  0.046   0.193    496
  Planarity :  0.004   0.039    585
  Dihedral  :  5.335  33.228    523
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.38 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.37 (0.43), residues: 412
  helix: -2.92 (1.00), residues: 21
  sheet:  0.08 (0.44), residues: 142
  loop :  0.83 (0.42), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H  36 
 HIS   0.003   0.002   HIS A 519 
 PHE   0.017   0.002   PHE H  29 
 TYR   0.011   0.002   TYR A 453 
 ARG   0.002   0.000   ARG L  55 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00412 (    1)
  link_NAG-ASN         : angle       1.62724 (    3)
  link_BETA1-4         : bond        0.00800 (    2)
  link_BETA1-4         : angle       2.70826 (    6)
  hydrogen bonds       : bond        0.03603 (  117)
  hydrogen bonds       : angle       6.11050 (  285)
  SS BOND              : bond        0.00250 (    6)
  SS BOND              : angle       1.36323 (   12)
  covalent geometry    : bond        0.00445 ( 3332)
  covalent geometry    : angle       0.70587 ( 4539)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2990.07 seconds
wall clock time: 55 minutes 37.65 seconds (3337.65 seconds total)