Starting phenix.real_space_refine
on Sun Apr 27 09:25:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zhg_60102/04_2025/8zhg_60102.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zhg_60102/04_2025/8zhg_60102.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zhg_60102/04_2025/8zhg_60102.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zhg_60102/04_2025/8zhg_60102.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zhg_60102/04_2025/8zhg_60102.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zhg_60102/04_2025/8zhg_60102.cif"
  }
  resolution = 3.51
  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=   0.040
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2345 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    2100      2.51       5
     N     556      2.21       5
     O     655      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3326
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 1552
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1552
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 11, 'TRANS': 184}
    Chain: "H"
      Number of atoms: 926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 926
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
    Chain: "L"
      Number of atoms: 820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 820
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 6, 'TRANS': 102}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 2.56, per 1000 atoms: 0.77
  Number of scatterers: 3326
  At special positions: 0
  Unit cell: (71.1776, 88.972, 79.3904, 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     655      8.00
     N     556      7.00
     C    2100      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    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 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  91 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
    NAG-ASN
      " NAG A   1 " - " ASN C 343 "
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 419.0 milliseconds
  

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  770

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 7 sheets defined
      8.7% alpha, 32.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'C' and resid 337 through 343
      removed outlier: 3.895A  pdb=" N   VAL C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   PHE C 342 " --> pdb=" O   PHE C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 383 through 387
      removed outlier: 3.611A  pdb=" N   LYS C 386 " --> pdb=" O   SER C 383 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 411
      removed outlier: 3.567A  pdb=" N   ILE C 410 " --> pdb=" O   GLU C 406 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ALA C 411 " --> pdb=" O   VAL C 407 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 406 through 411'
    Processing helix  chain 'C' and resid 502 through 505
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.926A  pdb=" N   SER H  31 " --> pdb=" O   THR H  28 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 28 through 32'
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.625A  pdb=" N   ASP H  90 " --> pdb=" O   ARG H  87 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   THR H  91 " --> pdb=" O   ALA H  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 87 through 91'
    Processing helix  chain 'L' and resid 82 through 86
      removed outlier: 3.509A  pdb=" N   ASP L  85 " --> pdb=" O   LYS L  82 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   GLU L  86 " --> pdb=" O   THR L  83 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 82 through 86'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.817A  pdb=" N   ASN C 354 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   SER C 399 " --> pdb=" O   ASN C 354 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLU C 516 " --> pdb=" O   ASN C 394 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   VAL C 433 " --> pdb=" O   PHE C 377 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   PHE C 377 " --> pdb=" O   VAL C 433 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   ALA C 435 " --> pdb=" O   SER C 375 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 17 through 23
    Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 59
      removed outlier: 4.874A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 5.992A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLN H  39 " --> pdb=" O   VAL H  93 " (cutoff:3.500A)
      removed outlier: 7.456A  pdb=" N   CYS H  96 " --> pdb=" O   TRP H 110 " (cutoff:3.500A)
      removed outlier: 5.590A  pdb=" N   TRP H 110 " --> pdb=" O   CYS H  96 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   ARG H  98 " --> pdb=" O   ASP H 108 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 58 through 59
      removed outlier: 4.874A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 5.992A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLN H  39 " --> pdb=" O   VAL H  93 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   THR H 114 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 5
    Processing sheet with id=AA6, first strand: chain 'L' and resid 46 through 49
      removed outlier: 3.965A  pdb=" N   VAL L  48 " --> pdb=" O   TRP L  36 " (cutoff:3.500A)
      removed outlier: 7.487A  pdb=" N   TRP L  36 " --> pdb=" O   VAL L  48 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   TYR L  90 " --> pdb=" O   TYR L  37 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLN L  39 " --> pdb=" O   ASP L  88 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 46 through 49
      removed outlier: 3.965A  pdb=" N   VAL L  48 " --> pdb=" O   TRP L  36 " (cutoff:3.500A)
      removed outlier: 7.487A  pdb=" N   TRP L  36 " --> pdb=" O   VAL L  48 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   TYR L  90 " --> pdb=" O   TYR L  37 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLN L  39 " --> pdb=" O   ASP L  88 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   TYR L  89 " --> pdb=" O   THR L 105 " (cutoff:3.500A)

    88 hydrogen bonds defined for protein.
    216 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.76

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 1070
        1.35 -     1.47: 932
        1.47 -     1.59: 1391
        1.59 -     1.71: 0
        1.71 -     1.84: 18
  Bond restraints: 3411
  Sorted by residual:
  bond pdb=" N   TYR C 473 "
       pdb=" CA  TYR C 473 "
    ideal  model  delta    sigma   weight residual
    1.455  1.484 -0.030 1.27e-02 6.20e+03 5.42e+00
  bond pdb=" C1  NAG A   2 "
       pdb=" O5  NAG A   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.73e+00
  bond pdb=" C1  NAG A   1 "
       pdb=" O5  NAG A   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.26e+00
  bond pdb=" CB  GLU L  86 "
       pdb=" CG  GLU L  86 "
    ideal  model  delta    sigma   weight residual
    1.520  1.564 -0.044 3.00e-02 1.11e+03 2.11e+00
  bond pdb=" C   TYR C 473 "
       pdb=" O   TYR C 473 "
    ideal  model  delta    sigma   weight residual
    1.234  1.251 -0.017 1.27e-02 6.20e+03 1.88e+00
  ... (remaining 3406 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 4447
        1.40 -     2.80: 153
        2.80 -     4.20: 26
        4.20 -     5.61: 8
        5.61 -     7.01: 5
  Bond angle restraints: 4639
  Sorted by residual:
  angle pdb=" CB  GLU L  86 "
        pdb=" CG  GLU L  86 "
        pdb=" CD  GLU L  86 "
      ideal   model   delta    sigma   weight residual
     112.60  118.01   -5.41 1.70e+00 3.46e-01 1.01e+01
  angle pdb=" CA  LYS H  43 "
        pdb=" CB  LYS H  43 "
        pdb=" CG  LYS H  43 "
      ideal   model   delta    sigma   weight residual
     114.10  120.30   -6.20 2.00e+00 2.50e-01 9.62e+00
  angle pdb=" C   CYS C 480 "
        pdb=" N   ASN C 481 "
        pdb=" CA  ASN C 481 "
      ideal   model   delta    sigma   weight residual
     121.54  127.17   -5.63 1.91e+00 2.74e-01 8.68e+00
  angle pdb=" CA  GLU L  86 "
        pdb=" CB  GLU L  86 "
        pdb=" CG  GLU L  86 "
      ideal   model   delta    sigma   weight residual
     114.10  119.36   -5.26 2.00e+00 2.50e-01 6.92e+00
  angle pdb=" CA  LYS L  16 "
        pdb=" CB  LYS L  16 "
        pdb=" CG  LYS L  16 "
      ideal   model   delta    sigma   weight residual
     114.10  119.22   -5.12 2.00e+00 2.50e-01 6.55e+00
  ... (remaining 4634 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.23: 1709
       17.23 -    34.45: 227
       34.45 -    51.68: 67
       51.68 -    68.91: 13
       68.91 -    86.14: 7
  Dihedral angle restraints: 2023
    sinusoidal: 803
      harmonic: 1220
  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
      93.00   60.96   32.04     1      1.00e+01 1.00e-02 1.46e+01
  dihedral pdb=" CA  ASP L  68 "
           pdb=" CB  ASP L  68 "
           pdb=" CG  ASP L  68 "
           pdb=" OD1 ASP L  68 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.46   59.46     1      2.00e+01 2.50e-03 1.18e+01
  dihedral pdb=" CB  CYS C 391 "
           pdb=" SG  CYS C 391 "
           pdb=" SG  CYS C 525 "
           pdb=" CB  CYS C 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   66.49   26.51     1      1.00e+01 1.00e-02 1.01e+01
  ... (remaining 2020 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 303
       0.033 -    0.067: 136
       0.067 -    0.100: 36
       0.100 -    0.133: 20
       0.133 -    0.166: 2
  Chirality restraints: 497
  Sorted by residual:
  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   -2.42   -0.17 2.00e-01 2.50e+01 6.91e-01
  chirality pdb=" CG  LEU C 452 "
            pdb=" CB  LEU C 452 "
            pdb=" CD1 LEU C 452 "
            pdb=" CD2 LEU C 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.39e-01
  chirality pdb=" CB  ILE L  49 "
            pdb=" CA  ILE L  49 "
            pdb=" CG1 ILE L  49 "
            pdb=" CG2 ILE L  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.35e-01
  ... (remaining 494 not shown)

  Planarity restraints: 603
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L  13 "   -0.059 5.00e-02 4.00e+02   8.98e-02 1.29e+01
        pdb=" N   PRO L  14 "    0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO L  14 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO L  14 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 462 "    0.035 5.00e-02 4.00e+02   5.34e-02 4.57e+00
        pdb=" N   PRO C 463 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO C 463 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 463 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 520 "    0.022 5.00e-02 4.00e+02   3.38e-02 1.83e+00
        pdb=" N   PRO C 521 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO C 521 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 521 "    0.019 5.00e-02 4.00e+02
  ... (remaining 600 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 888
        2.80 -     3.32: 2682
        3.32 -     3.85: 5331
        3.85 -     4.37: 5856
        4.37 -     4.90: 10330
  Nonbonded interactions: 25087
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 442 "
            pdb=" OH  TYR C 451 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" OG1 THR C 415 "
            pdb=" OD1 ASP C 420 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OD2 ASP C 398 "
            pdb=" OH  TYR C 423 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" OG1 THR C 430 "
            pdb=" O   PHE C 515 "
     model   vdw
     2.347 3.040
  nonbonded pdb=" OE1 GLU H  57 "
            pdb=" OH  TYR H  59 "
     model   vdw
     2.353 3.040
  ... (remaining 25082 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:             1.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.740
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6970
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      :  0.003   0.051   3419  Z= 0.152
  Angle     :  0.662   7.007   4657  Z= 0.337
  Chirality :  0.044   0.166    497
  Planarity :  0.007   0.090    602
  Dihedral  : 17.545  86.137   1235
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 32.69 %
    Favored  : 66.20 %
  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: -1.47 (0.40), residues: 419
  helix: -4.79 (0.32), residues: 19
  sheet:  1.06 (0.51), residues: 119
  loop : -1.75 (0.34), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP H 110 
 HIS   0.002   0.001   HIS L   8 
 PHE   0.009   0.001   PHE C 456 
 TYR   0.019   0.001   TYR C 453 
 ARG   0.009   0.001   ARG L  40 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00118 (    1)
  link_NAG-ASN         : angle       1.54311 (    3)
  link_BETA1-4         : bond        0.00445 (    1)
  link_BETA1-4         : angle       0.89168 (    3)
  hydrogen bonds       : bond        0.32078 (   71)
  hydrogen bonds       : angle      10.83789 (  216)
  SS BOND              : bond        0.00150 (    6)
  SS BOND              : angle       1.57542 (   12)
  covalent geometry    : bond        0.00333 ( 3411)
  covalent geometry    : angle       0.65737 ( 4639)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.355 
Fit side-chains
REVERT: C  465 GLU cc_start: 0.6576 (mt-10) cc_final: 0.6116 (mt-10)
REVERT: H  115 LEU cc_start: 0.8755 (tp) cc_final: 0.8505 (tt)
  outliers start: 4
  outliers final: 2
  residues processed: 50
  average time/residue: 0.2303
  time to fit residues: 13.5314
Evaluate side-chains
  46 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  427 ASP
Chi-restraints excluded: chain H residue   77 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0170
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.1980
   chunk 12 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0010
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.4024

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

Flipped N/Q/H residues before XYZ refinement:
C 437 ASN
C 506 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.172436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.138901 restraints weight = 4003.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.141933 restraints weight = 2733.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.144104 restraints weight = 2165.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.1775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3419  Z= 0.149
  Angle     :  0.542   4.744   4657  Z= 0.288
  Chirality :  0.043   0.143    497
  Planarity :  0.006   0.070    602
  Dihedral  :  4.481  41.055    514
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 26.87 %
    Favored  : 68.14 %
  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: -1.47 (0.39), residues: 419
  helix: -4.54 (0.50), residues: 18
  sheet:  0.54 (0.47), residues: 131
  loop : -1.60 (0.34), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 436 
 HIS   0.001   0.000   HIS L   8 
 PHE   0.013   0.001   PHE C 429 
 TYR   0.016   0.001   TYR C 495 
 ARG   0.007   0.001   ARG C 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00027 (    1)
  link_NAG-ASN         : angle       1.55123 (    3)
  link_BETA1-4         : bond        0.00256 (    1)
  link_BETA1-4         : angle       1.03810 (    3)
  hydrogen bonds       : bond        0.04111 (   71)
  hydrogen bonds       : angle       6.42248 (  216)
  SS BOND              : bond        0.00315 (    6)
  SS BOND              : angle       1.17567 (   12)
  covalent geometry    : bond        0.00338 ( 3411)
  covalent geometry    : angle       0.53797 ( 4639)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 45
  time to evaluate  : 0.333 
Fit side-chains
REVERT: C  346 ARG cc_start: 0.7337 (mtp85) cc_final: 0.6932 (mtp85)
REVERT: L   10 VAL cc_start: 0.4448 (OUTLIER) cc_final: 0.4247 (p)
  outliers start: 18
  outliers final: 11
  residues processed: 58
  average time/residue: 0.1505
  time to fit residues: 10.8022
Evaluate side-chains
  52 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  495 TYR
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain L residue   10 VAL
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   22 CYS
Chi-restraints excluded: chain L residue   48 VAL
Chi-restraints excluded: chain L residue   59 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
C 334 ASN
C 437 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.158560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.127185 restraints weight = 4043.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.128091 restraints weight = 3183.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.129391 restraints weight = 2835.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   3419  Z= 0.215
  Angle     :  0.634   5.635   4657  Z= 0.333
  Chirality :  0.045   0.136    497
  Planarity :  0.006   0.072    602
  Dihedral  :  4.294  14.081    510
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  6.93 %
    Allowed  : 28.25 %
    Favored  : 64.82 %
  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: -1.59 (0.39), residues: 419
  helix: -4.66 (0.45), residues: 18
  sheet:  0.51 (0.47), residues: 134
  loop : -1.73 (0.34), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  47 
 HIS   0.002   0.001   HIS L   8 
 PHE   0.024   0.002   PHE C 429 
 TYR   0.032   0.002   TYR C 495 
 ARG   0.003   0.001   ARG C 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00286 (    1)
  link_NAG-ASN         : angle       2.26233 (    3)
  link_BETA1-4         : bond        0.00266 (    1)
  link_BETA1-4         : angle       1.19794 (    3)
  hydrogen bonds       : bond        0.04647 (   71)
  hydrogen bonds       : angle       5.84206 (  216)
  SS BOND              : bond        0.00437 (    6)
  SS BOND              : angle       1.60903 (   12)
  covalent geometry    : bond        0.00528 ( 3411)
  covalent geometry    : angle       0.62640 ( 4639)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 45
  time to evaluate  : 0.359 
Fit side-chains
REVERT: C  334 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7557 (p0)
REVERT: C  346 ARG cc_start: 0.7539 (mtp85) cc_final: 0.7134 (mtp85)
REVERT: C  430 THR cc_start: 0.8713 (p) cc_final: 0.8478 (p)
REVERT: C  516 GLU cc_start: 0.7886 (pm20) cc_final: 0.7206 (pt0)
REVERT: H  100 GLN cc_start: 0.8234 (tt0) cc_final: 0.8001 (tt0)
REVERT: L   53 ASN cc_start: 0.6493 (m-40) cc_final: 0.6223 (p0)
REVERT: L   97 SER cc_start: 0.7685 (m) cc_final: 0.7318 (p)
  outliers start: 25
  outliers final: 19
  residues processed: 67
  average time/residue: 0.1817
  time to fit residues: 14.7029
Evaluate side-chains
  64 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 44
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  334 ASN
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  445 VAL
Chi-restraints excluded: chain C residue  456 PHE
Chi-restraints excluded: chain C residue  495 TYR
Chi-restraints excluded: chain C residue  524 VAL
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue   77 ASN
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   22 CYS
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0980
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** C 409 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 = 0.3749 r_free = 0.3749 target = 0.159621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.127161 restraints weight = 4115.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.127659 restraints weight = 3358.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.128798 restraints weight = 2613.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.3378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3419  Z= 0.165
  Angle     :  0.582   5.608   4657  Z= 0.305
  Chirality :  0.044   0.137    497
  Planarity :  0.005   0.067    602
  Dihedral  :  4.154  14.096    510
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 28.25 %
    Favored  : 65.65 %
  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: -1.50 (0.39), residues: 419
  helix: -4.59 (0.50), residues: 18
  sheet:  0.54 (0.48), residues: 133
  loop : -1.65 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 436 
 HIS   0.001   0.000   HIS L   8 
 PHE   0.016   0.002   PHE C 429 
 TYR   0.026   0.002   TYR C 495 
 ARG   0.005   0.001   ARG H  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00210 (    1)
  link_NAG-ASN         : angle       2.16935 (    3)
  link_BETA1-4         : bond        0.00201 (    1)
  link_BETA1-4         : angle       1.15885 (    3)
  hydrogen bonds       : bond        0.03822 (   71)
  hydrogen bonds       : angle       5.49840 (  216)
  SS BOND              : bond        0.00564 (    6)
  SS BOND              : angle       1.37481 (   12)
  covalent geometry    : bond        0.00403 ( 3411)
  covalent geometry    : angle       0.57568 ( 4639)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 40
  time to evaluate  : 0.354 
Fit side-chains
REVERT: C  346 ARG cc_start: 0.7489 (mtp85) cc_final: 0.7088 (mtp85)
REVERT: C  430 THR cc_start: 0.8671 (p) cc_final: 0.8458 (p)
REVERT: C  495 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.5843 (t80)
REVERT: C  516 GLU cc_start: 0.7825 (pm20) cc_final: 0.7292 (pt0)
REVERT: L   53 ASN cc_start: 0.6247 (m-40) cc_final: 0.5875 (p0)
REVERT: L   97 SER cc_start: 0.7852 (m) cc_final: 0.7475 (p)
  outliers start: 22
  outliers final: 16
  residues processed: 60
  average time/residue: 0.1770
  time to fit residues: 12.8526
Evaluate side-chains
  56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  407 VAL
Chi-restraints excluded: chain C residue  434 ILE
Chi-restraints excluded: chain C residue  495 TYR
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain H residue   12 VAL
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   22 CYS
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   48 VAL
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0870
   chunk 3 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.160065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.127616 restraints weight = 3989.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.128717 restraints weight = 3769.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.129913 restraints weight = 2743.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.3664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3419  Z= 0.147
  Angle     :  0.565   5.678   4657  Z= 0.297
  Chirality :  0.043   0.138    497
  Planarity :  0.005   0.061    602
  Dihedral  :  4.111  19.478    510
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 29.09 %
    Favored  : 65.93 %
  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: -1.41 (0.39), residues: 419
  helix: -4.45 (0.55), residues: 18
  sheet:  0.73 (0.48), residues: 131
  loop : -1.64 (0.34), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 436 
 HIS   0.001   0.000   HIS L   8 
 PHE   0.016   0.001   PHE C 429 
 TYR   0.024   0.001   TYR C 495 
 ARG   0.004   0.000   ARG H  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00165 (    1)
  link_NAG-ASN         : angle       2.25677 (    3)
  link_BETA1-4         : bond        0.00349 (    1)
  link_BETA1-4         : angle       1.26251 (    3)
  hydrogen bonds       : bond        0.03561 (   71)
  hydrogen bonds       : angle       5.30250 (  216)
  SS BOND              : bond        0.00514 (    6)
  SS BOND              : angle       1.28324 (   12)
  covalent geometry    : bond        0.00356 ( 3411)
  covalent geometry    : angle       0.55841 ( 4639)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 41
  time to evaluate  : 0.356 
Fit side-chains
REVERT: C  346 ARG cc_start: 0.7402 (mtp85) cc_final: 0.6993 (mtp85)
REVERT: C  442 ASP cc_start: 0.8063 (m-30) cc_final: 0.7595 (m-30)
REVERT: C  495 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.5959 (t80)
REVERT: C  516 GLU cc_start: 0.7848 (pm20) cc_final: 0.7423 (pt0)
REVERT: H   86 LEU cc_start: 0.8210 (mm) cc_final: 0.7856 (mt)
  outliers start: 18
  outliers final: 16
  residues processed: 56
  average time/residue: 0.2076
  time to fit residues: 13.9857
Evaluate side-chains
  57 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 40
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  407 VAL
Chi-restraints excluded: chain C residue  434 ILE
Chi-restraints excluded: chain C residue  445 VAL
Chi-restraints excluded: chain C residue  456 PHE
Chi-restraints excluded: chain C residue  495 TYR
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain H residue   77 ASN
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain L residue   22 CYS
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   83 THR
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0040
   chunk 32 optimal weight:    0.0870
   chunk 24 optimal weight:    0.0070
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.3988

-------------------------------------------------------------------------------
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 = 0.3739 r_free = 0.3739 target = 0.159056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.126627 restraints weight = 4127.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.128343 restraints weight = 3179.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.129516 restraints weight = 2661.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.3751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3419  Z= 0.124
  Angle     :  0.551   6.846   4657  Z= 0.286
  Chirality :  0.043   0.138    497
  Planarity :  0.005   0.057    602
  Dihedral  :  4.049  19.719    510
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 27.42 %
    Favored  : 66.48 %
  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: -1.22 (0.40), residues: 419
  helix: -4.35 (0.58), residues: 18
  sheet:  0.87 (0.47), residues: 131
  loop : -1.52 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 436 
 HIS   0.001   0.000   HIS L   8 
 PHE   0.014   0.001   PHE C 429 
 TYR   0.020   0.001   TYR C 495 
 ARG   0.003   0.000   ARG C 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00116 (    1)
  link_NAG-ASN         : angle       2.13047 (    3)
  link_BETA1-4         : bond        0.00314 (    1)
  link_BETA1-4         : angle       1.21151 (    3)
  hydrogen bonds       : bond        0.03384 (   71)
  hydrogen bonds       : angle       5.20930 (  216)
  SS BOND              : bond        0.00498 (    6)
  SS BOND              : angle       1.19463 (   12)
  covalent geometry    : bond        0.00299 ( 3411)
  covalent geometry    : angle       0.54554 ( 4639)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 39
  time to evaluate  : 0.345 
Fit side-chains
REVERT: C  346 ARG cc_start: 0.7398 (mtp85) cc_final: 0.6986 (mtp85)
REVERT: C  442 ASP cc_start: 0.7996 (m-30) cc_final: 0.7633 (m-30)
REVERT: C  495 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.6238 (t80)
REVERT: C  516 GLU cc_start: 0.7905 (pm20) cc_final: 0.7533 (pt0)
REVERT: H   86 LEU cc_start: 0.8229 (mm) cc_final: 0.7860 (mt)
  outliers start: 22
  outliers final: 18
  residues processed: 57
  average time/residue: 0.2114
  time to fit residues: 14.2192
Evaluate side-chains
  56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 37
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  407 VAL
Chi-restraints excluded: chain C residue  434 ILE
Chi-restraints excluded: chain C residue  445 VAL
Chi-restraints excluded: chain C residue  495 TYR
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain L residue   22 CYS
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   48 VAL
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   83 THR
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0970
   chunk 1 optimal weight:    0.5980
   chunk 9 optimal weight:    0.4980
   chunk 23 optimal weight:    0.0070
   chunk 27 optimal weight:    2.9990
   chunk 24 optimal weight:    0.4980
   chunk 29 optimal weight:    0.4980
   chunk 22 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0170
   chunk 4 optimal weight:    0.3980
   overall best weight:    0.2034

-------------------------------------------------------------------------------
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 = 0.3785 r_free = 0.3785 target = 0.163076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.130677 restraints weight = 3970.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.132611 restraints weight = 3829.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.133617 restraints weight = 2702.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.3780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3419  Z= 0.093
  Angle     :  0.513   5.649   4657  Z= 0.267
  Chirality :  0.041   0.133    497
  Planarity :  0.005   0.052    602
  Dihedral  :  3.826  19.393    510
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 27.70 %
    Favored  : 67.31 %
  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: -1.05 (0.40), residues: 419
  helix: -4.29 (0.59), residues: 18
  sheet:  0.92 (0.47), residues: 131
  loop : -1.36 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 436 
 HIS   0.001   0.000   HIS L   8 
 PHE   0.011   0.001   PHE C 429 
 TYR   0.012   0.001   TYR C 495 
 ARG   0.008   0.001   ARG C 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00023 (    1)
  link_NAG-ASN         : angle       1.81964 (    3)
  link_BETA1-4         : bond        0.00398 (    1)
  link_BETA1-4         : angle       1.06962 (    3)
  hydrogen bonds       : bond        0.03004 (   71)
  hydrogen bonds       : angle       4.90970 (  216)
  SS BOND              : bond        0.00447 (    6)
  SS BOND              : angle       1.09780 (   12)
  covalent geometry    : bond        0.00216 ( 3411)
  covalent geometry    : angle       0.50764 ( 4639)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 41
  time to evaluate  : 0.359 
Fit side-chains
REVERT: C  346 ARG cc_start: 0.7421 (mtp85) cc_final: 0.7014 (mtp85)
REVERT: C  442 ASP cc_start: 0.7924 (m-30) cc_final: 0.7564 (m-30)
REVERT: C  454 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.8171 (ttm-80)
REVERT: C  495 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.6778 (t80)
REVERT: C  516 GLU cc_start: 0.7786 (pm20) cc_final: 0.7547 (pt0)
REVERT: H   86 LEU cc_start: 0.8219 (mm) cc_final: 0.7867 (mt)
REVERT: H  112 GLN cc_start: 0.6093 (mm-40) cc_final: 0.5870 (mm-40)
  outliers start: 18
  outliers final: 11
  residues processed: 56
  average time/residue: 0.1829
  time to fit residues: 12.3301
Evaluate side-chains
  49 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 37
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  407 VAL
Chi-restraints excluded: chain C residue  495 TYR
Chi-restraints excluded: chain H residue   77 ASN
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   48 VAL
Chi-restraints excluded: chain L residue   83 THR
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0060
   chunk 3 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0770
   overall best weight:    0.4154

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

Flipped N/Q/H residues before XYZ refinement:
H  50 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.159771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.125433 restraints weight = 4032.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.128233 restraints weight = 2811.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.130066 restraints weight = 2259.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.3965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3419  Z= 0.126
  Angle     :  0.544   5.540   4657  Z= 0.283
  Chirality :  0.042   0.138    497
  Planarity :  0.005   0.053    602
  Dihedral  :  3.956  18.672    510
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 27.15 %
    Favored  : 67.04 %
  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: -1.05 (0.40), residues: 419
  helix: -4.21 (0.57), residues: 19
  sheet:  0.72 (0.46), residues: 137
  loop : -1.28 (0.36), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 436 
 HIS   0.001   0.000   HIS L   8 
 PHE   0.013   0.001   PHE C 429 
 TYR   0.021   0.001   TYR C 495 
 ARG   0.008   0.001   ARG C 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00112 (    1)
  link_NAG-ASN         : angle       2.15093 (    3)
  link_BETA1-4         : bond        0.00333 (    1)
  link_BETA1-4         : angle       1.17587 (    3)
  hydrogen bonds       : bond        0.03321 (   71)
  hydrogen bonds       : angle       4.92440 (  216)
  SS BOND              : bond        0.00465 (    6)
  SS BOND              : angle       1.17587 (   12)
  covalent geometry    : bond        0.00304 ( 3411)
  covalent geometry    : angle       0.53811 ( 4639)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 39
  time to evaluate  : 0.345 
Fit side-chains
REVERT: C  346 ARG cc_start: 0.7403 (mtp85) cc_final: 0.6994 (mtp85)
REVERT: C  442 ASP cc_start: 0.8006 (m-30) cc_final: 0.7612 (m-30)
REVERT: C  495 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.6287 (t80)
REVERT: C  516 GLU cc_start: 0.7909 (pm20) cc_final: 0.7644 (pt0)
  outliers start: 21
  outliers final: 17
  residues processed: 56
  average time/residue: 0.2056
  time to fit residues: 13.8181
Evaluate side-chains
  56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 38
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  407 VAL
Chi-restraints excluded: chain C residue  434 ILE
Chi-restraints excluded: chain C residue  495 TYR
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   67 ARG
Chi-restraints excluded: chain H residue   77 ASN
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   48 VAL
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   83 THR
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 36 optimal weight:    0.0870
   chunk 26 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0270
   chunk 0 optimal weight:    0.0980
   chunk 13 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.3016

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.166347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.133920 restraints weight = 4023.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.136334 restraints weight = 3667.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.137607 restraints weight = 2356.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.4016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3419  Z= 0.108
  Angle     :  0.527   5.180   4657  Z= 0.276
  Chirality :  0.042   0.157    497
  Planarity :  0.005   0.051    602
  Dihedral  :  3.880  18.153    510
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 28.25 %
    Favored  : 66.76 %
  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: -0.98 (0.40), residues: 419
  helix: -4.11 (0.61), residues: 19
  sheet:  0.73 (0.46), residues: 137
  loop : -1.19 (0.37), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 436 
 HIS   0.001   0.000   HIS L   8 
 PHE   0.011   0.001   PHE C 429 
 TYR   0.016   0.001   TYR C 495 
 ARG   0.007   0.001   ARG C 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00007 (    1)
  link_NAG-ASN         : angle       1.92165 (    3)
  link_BETA1-4         : bond        0.00372 (    1)
  link_BETA1-4         : angle       1.11169 (    3)
  hydrogen bonds       : bond        0.03113 (   71)
  hydrogen bonds       : angle       4.84253 (  216)
  SS BOND              : bond        0.00468 (    6)
  SS BOND              : angle       1.16542 (   12)
  covalent geometry    : bond        0.00257 ( 3411)
  covalent geometry    : angle       0.52203 ( 4639)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 39
  time to evaluate  : 0.331 
Fit side-chains
REVERT: C  346 ARG cc_start: 0.7399 (mtp85) cc_final: 0.6978 (mtp85)
REVERT: C  442 ASP cc_start: 0.7840 (m-30) cc_final: 0.7560 (m-30)
REVERT: C  495 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.6411 (t80)
REVERT: C  516 GLU cc_start: 0.7858 (pm20) cc_final: 0.7645 (pt0)
  outliers start: 18
  outliers final: 17
  residues processed: 53
  average time/residue: 0.1984
  time to fit residues: 12.5719
Evaluate side-chains
  57 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 39
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  407 VAL
Chi-restraints excluded: chain C residue  434 ILE
Chi-restraints excluded: chain C residue  495 TYR
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   77 ASN
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   48 VAL
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   83 THR
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    0.0010
   chunk 0 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 34 optimal weight:    0.4980
   chunk 38 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 28 optimal weight:    0.6980
   chunk 7 optimal weight:    0.2980
   overall best weight:    0.4386

-------------------------------------------------------------------------------
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 = 0.3742 r_free = 0.3742 target = 0.159195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.127440 restraints weight = 4065.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.128343 restraints weight = 3523.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.129431 restraints weight = 2790.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.4138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3419  Z= 0.130
  Angle     :  0.549   5.358   4657  Z= 0.288
  Chirality :  0.043   0.155    497
  Planarity :  0.005   0.052    602
  Dihedral  :  3.981  17.682    510
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 27.70 %
    Favored  : 67.04 %
  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: -1.00 (0.40), residues: 419
  helix: -4.14 (0.59), residues: 19
  sheet:  0.74 (0.46), residues: 137
  loop : -1.22 (0.37), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 436 
 HIS   0.001   0.000   HIS L   8 
 PHE   0.012   0.001   PHE C 429 
 TYR   0.021   0.001   TYR C 495 
 ARG   0.007   0.001   ARG C 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00115 (    1)
  link_NAG-ASN         : angle       2.18214 (    3)
  link_BETA1-4         : bond        0.00304 (    1)
  link_BETA1-4         : angle       1.18309 (    3)
  hydrogen bonds       : bond        0.03323 (   71)
  hydrogen bonds       : angle       4.87437 (  216)
  SS BOND              : bond        0.00486 (    6)
  SS BOND              : angle       1.19885 (   12)
  covalent geometry    : bond        0.00314 ( 3411)
  covalent geometry    : angle       0.54302 ( 4639)

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

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

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  838 Ramachandran restraints generated.
    419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 39
  time to evaluate  : 0.362 
Fit side-chains
REVERT: C  346 ARG cc_start: 0.7439 (mtp85) cc_final: 0.7100 (mtp85)
REVERT: C  442 ASP cc_start: 0.7887 (m-30) cc_final: 0.7521 (m-30)
REVERT: C  490 PHE cc_start: 0.7600 (t80) cc_final: 0.7355 (t80)
REVERT: C  495 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.6201 (t80)
REVERT: C  516 GLU cc_start: 0.7969 (pm20) cc_final: 0.7742 (pt0)
  outliers start: 19
  outliers final: 16
  residues processed: 54
  average time/residue: 0.1746
  time to fit residues: 11.4116
Evaluate side-chains
  56 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  358 ILE
Chi-restraints excluded: chain C residue  367 VAL
Chi-restraints excluded: chain C residue  399 SER
Chi-restraints excluded: chain C residue  407 VAL
Chi-restraints excluded: chain C residue  434 ILE
Chi-restraints excluded: chain C residue  495 TYR
Chi-restraints excluded: chain C residue  517 LEU
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   77 ASN
Chi-restraints excluded: chain H residue  115 LEU
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   49 ILE
Chi-restraints excluded: chain L residue   59 VAL
Chi-restraints excluded: chain L residue   78 ILE
Chi-restraints excluded: chain L residue   83 THR
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 37 optimal weight:    0.3980
   chunk 1 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3741 r_free = 0.3741 target = 0.158972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.125097 restraints weight = 4074.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.127810 restraints weight = 2859.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.129275 restraints weight = 2306.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.4360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3419  Z= 0.160
  Angle     :  0.588   6.111   4657  Z= 0.309
  Chirality :  0.044   0.165    497
  Planarity :  0.005   0.055    602
  Dihedral  :  4.252  17.049    510
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 28.25 %
    Favored  : 67.04 %
  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: -1.27 (0.40), residues: 419
  helix: -4.33 (0.45), residues: 25
  sheet:  0.66 (0.46), residues: 138
  loop : -1.41 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 436 
 HIS   0.001   0.001   HIS L   8 
 PHE   0.013   0.001   PHE C 429 
 TYR   0.026   0.002   TYR C 495 
 ARG   0.008   0.001   ARG C 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00176 (    1)
  link_NAG-ASN         : angle       2.36938 (    3)
  link_BETA1-4         : bond        0.00234 (    1)
  link_BETA1-4         : angle       1.18903 (    3)
  hydrogen bonds       : bond        0.03555 (   71)
  hydrogen bonds       : angle       5.01688 (  216)
  SS BOND              : bond        0.00544 (    6)
  SS BOND              : angle       1.28796 (   12)
  covalent geometry    : bond        0.00392 ( 3411)
  covalent geometry    : angle       0.58119 ( 4639)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1702.43 seconds
wall clock time: 30 minutes 17.76 seconds (1817.76 seconds total)