Starting phenix.real_space_refine
on Wed Jul 23 13:56:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wr8_32718/07_2025/7wr8_32718.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wr8_32718/07_2025/7wr8_32718.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wr8_32718/07_2025/7wr8_32718.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wr8_32718/07_2025/7wr8_32718.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wr8_32718/07_2025/7wr8_32718.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wr8_32718/07_2025/7wr8_32718.cif"
  }
  resolution = 3.5
  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=   0.026
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    2086      2.51       5
     N     555      2.21       5
     O     630      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 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: 3286
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "R"
      Number of atoms: 1504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1504
          Classifications: {'peptide': 187}
          Link IDs: {'PTRANS': 10, 'TRANS': 176}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 964
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 6, 'TRANS': 119}
    Chain: "B"
      Number of atoms: 780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 780
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 9, 'TRANS': 94}
    Chain: "C"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 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: 3.46, per 1000 atoms: 1.05
  Number of scatterers: 3286
  At special positions: 0
  Unit cell: (100.88, 62.4, 69.68, 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     630      8.00
     N     555      7.00
     C    2086      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 336 " - pdb=" SG  CYS R 361 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R 379 " - pdb=" SG  CYS R 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 391 " - pdb=" SG  CYS R 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  87 " 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 C   1 " - " NAG C   2 "
    BETA1-6
      " NAG C   1 " - " FUC C   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG C   1 " - " ASN R 343 "
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 403.8 milliseconds
  

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  760

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 8 sheets defined
      9.6% alpha, 22.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'R' and resid 338 through 343
    Processing helix  chain 'R' and resid 349 through 353
      removed outlier: 3.925A  pdb=" N   TRP R 353 " --> pdb=" O   VAL R 350 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 364 through 369
      removed outlier: 4.319A  pdb=" N   VAL R 367 " --> pdb=" O   ASP R 364 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   TYR R 369 " --> pdb=" O   SER R 366 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 383 through 387
      removed outlier: 3.912A  pdb=" N   LEU R 387 " --> pdb=" O   PRO R 384 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 405 through 407
      No H-bonds generated for 'chain 'R' and resid 405 through 407'
    Processing helix  chain 'R' and resid 417 through 422
    Processing helix  chain 'A' and resid 62 through 65
      removed outlier: 3.804A  pdb=" N   GLN A  65 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 62 through 65'
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.668A  pdb=" N   THR A  91 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358
      removed outlier: 3.631A  pdb=" N   LYS R 356 " --> pdb=" O   ALA R 397 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'R' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'A' and resid 3 through 6
      removed outlier: 4.353A  pdb=" N   GLN A   3 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   SER A  25 " --> pdb=" O   GLN A   3 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 16 through 18
      removed outlier: 3.522A  pdb=" N   SER A  17 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   LEU A  83 " --> pdb=" O   SER A  17 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 60
      removed outlier: 5.146A  pdb=" N   TRP A  47 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ARG A  38 " --> pdb=" O   TRP A  47 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 5
      removed outlier: 3.857A  pdb=" N   THR B  73 " --> pdb=" O   SER B  62 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   SER B  62 " --> pdb=" O   THR B  73 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 9 through 11
      removed outlier: 3.891A  pdb=" N   THR B 103 " --> pdb=" O   TYR B  85 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   GLN B  36 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   LEU B  45 " --> pdb=" O   GLN B  36 " (cutoff:3.500A)

    74 hydrogen bonds defined for protein.
    174 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: 0.78

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 813
        1.33 -     1.45: 759
        1.45 -     1.57: 1783
        1.57 -     1.69: 0
        1.69 -     1.81: 18
  Bond restraints: 3373
  Sorted by residual:
  bond pdb=" CG  LEU R 441 "
       pdb=" CD2 LEU R 441 "
    ideal  model  delta    sigma   weight residual
    1.521  1.437  0.084 3.30e-02 9.18e+02 6.50e+00
  bond pdb=" C   GLU B  52 "
       pdb=" N   ARG B  53 "
    ideal  model  delta    sigma   weight residual
    1.331  1.308  0.023 1.05e-02 9.07e+03 4.83e+00
  bond pdb=" C   ASP A 105 "
       pdb=" N   PRO A 106 "
    ideal  model  delta    sigma   weight residual
    1.334  1.379 -0.045 2.34e-02 1.83e+03 3.72e+00
  bond pdb=" C   SER B  13 "
       pdb=" N   PRO B  14 "
    ideal  model  delta    sigma   weight residual
    1.332  1.357 -0.026 1.34e-02 5.57e+03 3.63e+00
  bond pdb=" CB  TRP A  47 "
       pdb=" CG  TRP A  47 "
    ideal  model  delta    sigma   weight residual
    1.498  1.442  0.056 3.10e-02 1.04e+03 3.21e+00
  ... (remaining 3368 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.43: 4546
        4.43 -     8.86: 45
        8.86 -    13.29: 1
       13.29 -    17.72: 0
       17.72 -    22.15: 1
  Bond angle restraints: 4593
  Sorted by residual:
  angle pdb=" CA  LEU B  27 "
        pdb=" CB  LEU B  27 "
        pdb=" CG  LEU B  27 "
      ideal   model   delta    sigma   weight residual
     116.30  138.45  -22.15 3.50e+00 8.16e-02 4.00e+01
  angle pdb=" CA  PRO R 373 "
        pdb=" C   PRO R 373 "
        pdb=" N   PHE R 374 "
      ideal   model   delta    sigma   weight residual
     116.20  120.25   -4.05 8.00e-01 1.56e+00 2.57e+01
  angle pdb=" N   ASN R 477 "
        pdb=" CA  ASN R 477 "
        pdb=" C   ASN R 477 "
      ideal   model   delta    sigma   weight residual
     110.97  116.45   -5.48 1.09e+00 8.42e-01 2.53e+01
  angle pdb=" CA  PRO R 373 "
        pdb=" C   PRO R 373 "
        pdb=" O   PRO R 373 "
      ideal   model   delta    sigma   weight residual
     121.31  118.05    3.26 7.40e-01 1.83e+00 1.94e+01
  angle pdb=" C   LYS B  49 "
        pdb=" N   ASP B  50 "
        pdb=" CA  ASP B  50 "
      ideal   model   delta    sigma   weight residual
     121.54  129.28   -7.74 1.91e+00 2.74e-01 1.64e+01
  ... (remaining 4588 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.93: 1763
       15.93 -    31.86: 206
       31.86 -    47.79: 45
       47.79 -    63.72: 2
       63.72 -    79.64: 4
  Dihedral angle restraints: 2020
    sinusoidal: 818
      harmonic: 1202
  Sorted by residual:
  dihedral pdb=" CA  SER B  93 "
           pdb=" C   SER B  93 "
           pdb=" N   THR B  94 "
           pdb=" CA  THR B  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.28   28.72     0      5.00e+00 4.00e-02 3.30e+01
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  87 "
           pdb=" CB  CYS B  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.57   45.43     1      1.00e+01 1.00e-02 2.86e+01
  dihedral pdb=" CA  ASP A 105 "
           pdb=" C   ASP A 105 "
           pdb=" N   PRO A 106 "
           pdb=" CA  PRO A 106 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.94  -24.06     0      5.00e+00 4.00e-02 2.32e+01
  ... (remaining 2017 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 342
       0.052 -    0.105: 108
       0.105 -    0.157: 42
       0.157 -    0.210: 6
       0.210 -    0.262: 4
  Chirality restraints: 502
  Sorted by residual:
  chirality pdb=" C1  FUC C   3 "
            pdb=" O6  NAG C   1 "
            pdb=" C2  FUC C   3 "
            pdb=" O5  FUC C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.51    0.11 2.00e-02 2.50e+03 3.18e+01
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.49    0.09 2.00e-02 2.50e+03 1.90e+01
  chirality pdb=" CB  ILE A  19 "
            pdb=" CA  ILE A  19 "
            pdb=" CG1 ILE A  19 "
            pdb=" CG2 ILE A  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.91   -0.26 2.00e-01 2.50e+01 1.72e+00
  ... (remaining 499 not shown)

  Planarity restraints: 592
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "   -0.136 2.00e-02 2.50e+03   1.11e-01 1.55e+02
        pdb=" C7  NAG C   1 "    0.038 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "   -0.102 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "    0.175 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 118 "   -0.019 2.00e-02 2.50e+03   3.89e-02 1.51e+01
        pdb=" C   VAL A 118 "    0.067 2.00e-02 2.50e+03
        pdb=" O   VAL A 118 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   TRP A 119 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  27 "   -0.048 5.00e-02 4.00e+02   7.29e-02 8.49e+00
        pdb=" N   PRO B  28 "    0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO B  28 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B  28 "   -0.042 5.00e-02 4.00e+02
  ... (remaining 589 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 597
        2.76 -     3.30: 2775
        3.30 -     3.83: 5395
        3.83 -     4.37: 6177
        4.37 -     4.90: 11042
  Nonbonded interactions: 25986
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS R 440 "
            pdb=" N   SER A 104 "
     model   vdw
     2.230 3.200
  nonbonded pdb=" OG  SER R 359 "
            pdb=" OD1 ASN R 394 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   SER B  29 "
            pdb=" OG  SER B  29 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" NE2 HIS A  35 "
            pdb=" OD1 ASP A  99 "
     model   vdw
     2.307 3.120
  nonbonded pdb=" OH  TYR B  35 "
            pdb=" OE1 GLN B  88 "
     model   vdw
     2.328 3.040
  ... (remaining 25981 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:             3.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.830
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
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      :  0.008   0.084   3381  Z= 0.362
  Angle     :  1.165  22.149   4612  Z= 0.630
  Chirality :  0.062   0.262    502
  Planarity :  0.010   0.111    591
  Dihedral  : 13.718  79.644   1245
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.47 %
    Favored  : 87.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  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: -3.48 (0.38), residues: 409
  helix: -3.53 (0.89), residues: 21
  sheet: -1.93 (0.42), residues: 139
  loop : -2.50 (0.36), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP A  47 
 HIS   0.004   0.001   HIS A  32 
 PHE   0.050   0.004   PHE R 456 
 TYR   0.035   0.003   TYR R 501 
 ARG   0.015   0.002   ARG A  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00681 (    1)
  link_NAG-ASN         : angle       2.80445 (    3)
  link_BETA1-4         : bond        0.00141 (    1)
  link_BETA1-4         : angle       2.52464 (    3)
  hydrogen bonds       : bond        0.27290 (   74)
  hydrogen bonds       : angle      11.40966 (  174)
  link_BETA1-6         : bond        0.00991 (    1)
  link_BETA1-6         : angle       2.88496 (    3)
  SS BOND              : bond        0.00462 (    5)
  SS BOND              : angle       0.87019 (   10)
  covalent geometry    : bond        0.00829 ( 3373)
  covalent geometry    : angle       1.16026 ( 4593)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A   80 TYR cc_start: 0.7233 (m-80) cc_final: 0.7012 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.1574
  time to fit residues: 14.2487
Evaluate side-chains
  66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 30 optimal weight:    0.4980
   chunk 16 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3892 r_free = 0.3892 target = 0.173941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.145206 restraints weight = 3687.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.148947 restraints weight = 2586.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.151187 restraints weight = 2022.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.1380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3381  Z= 0.171
  Angle     :  0.702  10.891   4612  Z= 0.360
  Chirality :  0.046   0.138    502
  Planarity :  0.006   0.064    591
  Dihedral  :  6.695  27.478    524
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.02 %
    Favored  : 89.98 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  9.66 %
    Favored  : 88.92 %
  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: -3.20 (0.39), residues: 409
  helix: -3.77 (0.71), residues: 27
  sheet: -1.69 (0.42), residues: 144
  loop : -2.24 (0.39), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 119 
 HIS   0.001   0.001   HIS B  97 
 PHE   0.015   0.001   PHE A 101 
 TYR   0.018   0.001   TYR R 495 
 ARG   0.005   0.001   ARG R 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00267 (    1)
  link_NAG-ASN         : angle       1.72877 (    3)
  link_BETA1-4         : bond        0.00060 (    1)
  link_BETA1-4         : angle       1.90334 (    3)
  hydrogen bonds       : bond        0.04703 (   74)
  hydrogen bonds       : angle       7.01920 (  174)
  link_BETA1-6         : bond        0.00012 (    1)
  link_BETA1-6         : angle       2.35043 (    3)
  SS BOND              : bond        0.00552 (    5)
  SS BOND              : angle       0.98720 (   10)
  covalent geometry    : bond        0.00391 ( 3373)
  covalent geometry    : angle       0.69606 ( 4593)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A   87 ARG cc_start: 0.6892 (mtm-85) cc_final: 0.6585 (mtm-85)
  outliers start: 5
  outliers final: 4
  residues processed: 75
  average time/residue: 0.1862
  time to fit residues: 16.5068
Evaluate side-chains
  68 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  385 THR
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain B residue   23 SER
Chi-restraints excluded: chain B residue   91 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0870
   chunk 19 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.8360

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

Flipped N/Q/H residues before XYZ refinement:
R 409 GLN
B   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.173219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.146190 restraints weight = 3629.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.149633 restraints weight = 2601.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.152120 restraints weight = 2050.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3381  Z= 0.172
  Angle     :  0.669   8.807   4612  Z= 0.343
  Chirality :  0.046   0.142    502
  Planarity :  0.005   0.058    591
  Dihedral  :  6.273  28.153    524
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.25 %
    Favored  : 88.75 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 11.08 %
    Favored  : 86.93 %
  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: -3.18 (0.40), residues: 409
  helix: -4.18 (0.62), residues: 26
  sheet: -1.63 (0.43), residues: 144
  loop : -2.22 (0.39), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP R 436 
 HIS   0.002   0.001   HIS R 505 
 PHE   0.013   0.001   PHE A 101 
 TYR   0.018   0.001   TYR R 495 
 ARG   0.007   0.001   ARG R 454 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00194 (    1)
  link_NAG-ASN         : angle       1.51888 (    3)
  link_BETA1-4         : bond        0.00041 (    1)
  link_BETA1-4         : angle       1.63379 (    3)
  hydrogen bonds       : bond        0.04059 (   74)
  hydrogen bonds       : angle       6.42134 (  174)
  link_BETA1-6         : bond        0.00143 (    1)
  link_BETA1-6         : angle       2.31578 (    3)
  SS BOND              : bond        0.00308 (    5)
  SS BOND              : angle       0.97938 (   10)
  covalent geometry    : bond        0.00401 ( 3373)
  covalent geometry    : angle       0.66417 ( 4593)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.403 
Fit side-chains
REVERT: R  396 TYR cc_start: 0.7804 (m-80) cc_final: 0.7550 (m-80)
REVERT: B   91 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6720 (t0)
  outliers start: 7
  outliers final: 4
  residues processed: 73
  average time/residue: 0.1802
  time to fit residues: 15.9954
Evaluate side-chains
  73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  385 THR
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   91 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 31 optimal weight:    8.9990
   chunk 3 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   overall best weight:    1.0784

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.160688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.133668 restraints weight = 3912.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.134012 restraints weight = 3194.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.134971 restraints weight = 2991.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   3381  Z= 0.200
  Angle     :  0.666   7.767   4612  Z= 0.340
  Chirality :  0.046   0.129    502
  Planarity :  0.005   0.052    591
  Dihedral  :  6.070  27.994    524
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.71 %
    Favored  : 87.29 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 12.22 %
    Favored  : 84.94 %
  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: -3.15 (0.40), residues: 409
  helix: -4.25 (0.55), residues: 26
  sheet: -1.66 (0.43), residues: 143
  loop : -2.14 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP R 436 
 HIS   0.002   0.001   HIS R 505 
 PHE   0.020   0.002   PHE R 456 
 TYR   0.017   0.002   TYR R 495 
 ARG   0.005   0.001   ARG R 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00282 (    1)
  link_NAG-ASN         : angle       1.58713 (    3)
  link_BETA1-4         : bond        0.00049 (    1)
  link_BETA1-4         : angle       1.69755 (    3)
  hydrogen bonds       : bond        0.03689 (   74)
  hydrogen bonds       : angle       6.14413 (  174)
  link_BETA1-6         : bond        0.00242 (    1)
  link_BETA1-6         : angle       2.38947 (    3)
  SS BOND              : bond        0.00295 (    5)
  SS BOND              : angle       0.88382 (   10)
  covalent geometry    : bond        0.00470 ( 3373)
  covalent geometry    : angle       0.66029 ( 4593)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 1.468 
Fit side-chains
REVERT: R  396 TYR cc_start: 0.7852 (m-80) cc_final: 0.7601 (m-80)
REVERT: A  103 LEU cc_start: 0.5456 (OUTLIER) cc_final: 0.5084 (pp)
REVERT: B   91 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.6852 (t0)
  outliers start: 10
  outliers final: 6
  residues processed: 76
  average time/residue: 0.2185
  time to fit residues: 20.9917
Evaluate side-chains
  73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  385 THR
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain B residue    3 ASP
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue   91 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3787 r_free = 0.3787 target = 0.162664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.133172 restraints weight = 3849.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.136588 restraints weight = 2778.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.138792 restraints weight = 2225.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3381  Z= 0.168
  Angle     :  0.638   9.200   4612  Z= 0.323
  Chirality :  0.045   0.128    502
  Planarity :  0.005   0.056    591
  Dihedral  :  5.863  28.548    524
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.74 %
    Favored  : 88.26 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.34 %
    Favored  : 82.10 %
  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: -2.93 (0.41), residues: 409
  helix: -3.96 (0.70), residues: 20
  sheet: -1.63 (0.43), residues: 141
  loop : -1.99 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP R 436 
 HIS   0.002   0.001   HIS R 505 
 PHE   0.019   0.001   PHE R 456 
 TYR   0.016   0.001   TYR R 495 
 ARG   0.005   0.001   ARG A  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00139 (    1)
  link_NAG-ASN         : angle       1.09482 (    3)
  link_BETA1-4         : bond        0.00003 (    1)
  link_BETA1-4         : angle       1.40601 (    3)
  hydrogen bonds       : bond        0.03310 (   74)
  hydrogen bonds       : angle       5.97470 (  174)
  link_BETA1-6         : bond        0.00100 (    1)
  link_BETA1-6         : angle       2.13530 (    3)
  SS BOND              : bond        0.00389 (    5)
  SS BOND              : angle       0.85305 (   10)
  covalent geometry    : bond        0.00392 ( 3373)
  covalent geometry    : angle       0.63392 ( 4593)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.683 
Fit side-chains
REVERT: R  396 TYR cc_start: 0.7827 (m-80) cc_final: 0.7574 (m-80)
REVERT: A   80 TYR cc_start: 0.7051 (m-80) cc_final: 0.6736 (m-80)
REVERT: A  103 LEU cc_start: 0.5439 (OUTLIER) cc_final: 0.5060 (pp)
REVERT: B   91 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6987 (t0)
  outliers start: 9
  outliers final: 6
  residues processed: 72
  average time/residue: 0.3644
  time to fit residues: 33.3876
Evaluate side-chains
  72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  385 THR
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain B residue    3 ASP
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue   91 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 28 optimal weight:    0.0670
   chunk 20 optimal weight:    0.2980
   chunk 5 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.5918

-------------------------------------------------------------------------------
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 = 0.3800 r_free = 0.3800 target = 0.163854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.134034 restraints weight = 3917.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.137522 restraints weight = 2795.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.139752 restraints weight = 2222.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3381  Z= 0.137
  Angle     :  0.617   8.359   4612  Z= 0.312
  Chirality :  0.044   0.128    502
  Planarity :  0.005   0.047    591
  Dihedral  :  5.613  27.256    524
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.02 %
    Favored  : 89.98 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.62 %
    Favored  : 81.82 %
  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: -2.84 (0.41), residues: 409
  helix: -3.98 (0.68), residues: 20
  sheet: -1.53 (0.44), residues: 141
  loop : -1.95 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 436 
 HIS   0.001   0.000   HIS A  35 
 PHE   0.017   0.001   PHE R 456 
 TYR   0.015   0.001   TYR R 495 
 ARG   0.004   0.001   ARG A  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00131 (    1)
  link_NAG-ASN         : angle       1.01463 (    3)
  link_BETA1-4         : bond        0.00165 (    1)
  link_BETA1-4         : angle       1.26573 (    3)
  hydrogen bonds       : bond        0.03099 (   74)
  hydrogen bonds       : angle       5.82279 (  174)
  link_BETA1-6         : bond        0.00049 (    1)
  link_BETA1-6         : angle       1.95998 (    3)
  SS BOND              : bond        0.00225 (    5)
  SS BOND              : angle       0.77850 (   10)
  covalent geometry    : bond        0.00321 ( 3373)
  covalent geometry    : angle       0.61382 ( 4593)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 1.464 
Fit side-chains
REVERT: R  396 TYR cc_start: 0.7760 (m-80) cc_final: 0.7532 (m-80)
REVERT: A  103 LEU cc_start: 0.5390 (OUTLIER) cc_final: 0.5036 (pp)
REVERT: B   91 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6913 (t0)
  outliers start: 9
  outliers final: 6
  residues processed: 71
  average time/residue: 0.3226
  time to fit residues: 30.1226
Evaluate side-chains
  68 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain B residue    3 ASP
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue   91 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0070
   chunk 36 optimal weight:    1.9990
   chunk 4 optimal weight:    0.2980
   chunk 37 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.8000

-------------------------------------------------------------------------------
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 = 0.3779 r_free = 0.3779 target = 0.162024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.132627 restraints weight = 3843.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.135773 restraints weight = 2801.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.137808 restraints weight = 2265.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3381  Z= 0.160
  Angle     :  0.634   7.610   4612  Z= 0.322
  Chirality :  0.045   0.132    502
  Planarity :  0.005   0.050    591
  Dihedral  :  5.602  27.221    524
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.00 %
    Favored  : 89.00 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.19 %
    Favored  : 80.68 %
  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: -2.78 (0.41), residues: 409
  helix: -3.63 (0.94), residues: 14
  sheet: -1.53 (0.44), residues: 141
  loop : -1.98 (0.39), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 436 
 HIS   0.001   0.001   HIS R 505 
 PHE   0.018   0.001   PHE R 456 
 TYR   0.015   0.001   TYR R 495 
 ARG   0.006   0.001   ARG A  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00173 (    1)
  link_NAG-ASN         : angle       1.19907 (    3)
  link_BETA1-4         : bond        0.00030 (    1)
  link_BETA1-4         : angle       1.42021 (    3)
  hydrogen bonds       : bond        0.03152 (   74)
  hydrogen bonds       : angle       5.85970 (  174)
  link_BETA1-6         : bond        0.00164 (    1)
  link_BETA1-6         : angle       2.06219 (    3)
  SS BOND              : bond        0.00211 (    5)
  SS BOND              : angle       0.79720 (   10)
  covalent geometry    : bond        0.00377 ( 3373)
  covalent geometry    : angle       0.63014 ( 4593)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.780 
Fit side-chains
REVERT: R  374 PHE cc_start: 0.6351 (OUTLIER) cc_final: 0.5372 (t80)
REVERT: R  396 TYR cc_start: 0.7773 (m-80) cc_final: 0.7550 (m-80)
REVERT: A  103 LEU cc_start: 0.5449 (OUTLIER) cc_final: 0.5098 (pp)
REVERT: A  109 TRP cc_start: 0.9008 (m-10) cc_final: 0.8756 (m-10)
  outliers start: 11
  outliers final: 8
  residues processed: 72
  average time/residue: 0.1789
  time to fit residues: 16.0751
Evaluate side-chains
  72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  385 THR
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain B residue    3 ASP
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   64 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0980
   chunk 12 optimal weight:    3.9990
   chunk 26 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3796 r_free = 0.3796 target = 0.163317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.133558 restraints weight = 3849.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.136923 restraints weight = 2805.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.138906 restraints weight = 2253.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3381  Z= 0.146
  Angle     :  0.639  11.391   4612  Z= 0.319
  Chirality :  0.045   0.127    502
  Planarity :  0.005   0.045    591
  Dihedral  :  5.511  26.765    524
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.02 %
    Favored  : 89.98 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 16.48 %
    Favored  : 79.83 %
  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: -2.55 (0.42), residues: 409
  helix: -3.09 (1.79), residues: 6
  sheet: -1.48 (0.44), residues: 141
  loop : -1.83 (0.39), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 436 
 HIS   0.001   0.001   HIS A  35 
 PHE   0.022   0.001   PHE R 456 
 TYR   0.015   0.001   TYR R 495 
 ARG   0.006   0.001   ARG A  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00122 (    1)
  link_NAG-ASN         : angle       1.05679 (    3)
  link_BETA1-4         : bond        0.00131 (    1)
  link_BETA1-4         : angle       1.33181 (    3)
  hydrogen bonds       : bond        0.03071 (   74)
  hydrogen bonds       : angle       5.80495 (  174)
  link_BETA1-6         : bond        0.00134 (    1)
  link_BETA1-6         : angle       1.96465 (    3)
  SS BOND              : bond        0.00215 (    5)
  SS BOND              : angle       0.77873 (   10)
  covalent geometry    : bond        0.00343 ( 3373)
  covalent geometry    : angle       0.63602 ( 4593)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.537 
Fit side-chains
REVERT: R  374 PHE cc_start: 0.6231 (OUTLIER) cc_final: 0.5228 (t80)
REVERT: R  396 TYR cc_start: 0.7789 (m-80) cc_final: 0.7551 (m-80)
REVERT: A  103 LEU cc_start: 0.5366 (OUTLIER) cc_final: 0.5001 (pp)
REVERT: A  109 TRP cc_start: 0.8992 (m-10) cc_final: 0.8733 (m-10)
  outliers start: 13
  outliers final: 11
  residues processed: 74
  average time/residue: 0.2083
  time to fit residues: 18.9957
Evaluate side-chains
  74 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  385 THR
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain B residue    3 ASP
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue   71 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0980
   chunk 31 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0370
   chunk 38 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0670
   chunk 30 optimal weight:    0.5980
   chunk 20 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.3596

-------------------------------------------------------------------------------
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 = 0.3843 r_free = 0.3843 target = 0.167902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.136983 restraints weight = 3867.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.140414 restraints weight = 2818.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.143012 restraints weight = 2273.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   3381  Z= 0.129
  Angle     :  0.652  10.019   4612  Z= 0.327
  Chirality :  0.046   0.242    502
  Planarity :  0.005   0.049    591
  Dihedral  :  5.412  25.259    524
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.54 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 17.61 %
    Favored  : 78.98 %
  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: -2.41 (0.42), residues: 409
  helix: -3.02 (1.82), residues: 6
  sheet: -1.31 (0.45), residues: 135
  loop : -1.78 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 119 
 HIS   0.001   0.001   HIS R 505 
 PHE   0.021   0.001   PHE R 456 
 TYR   0.012   0.001   TYR R 495 
 ARG   0.006   0.001   ARG A  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00012 (    1)
  link_NAG-ASN         : angle       0.79443 (    3)
  link_BETA1-4         : bond        0.00232 (    1)
  link_BETA1-4         : angle       1.12662 (    3)
  hydrogen bonds       : bond        0.03128 (   74)
  hydrogen bonds       : angle       5.85118 (  174)
  link_BETA1-6         : bond        0.00033 (    1)
  link_BETA1-6         : angle       1.70771 (    3)
  SS BOND              : bond        0.00711 (    5)
  SS BOND              : angle       2.17393 (   10)
  covalent geometry    : bond        0.00314 ( 3373)
  covalent geometry    : angle       0.64273 ( 4593)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.437 
Fit side-chains
REVERT: R  396 TYR cc_start: 0.7750 (m-80) cc_final: 0.7532 (m-80)
REVERT: A  103 LEU cc_start: 0.5222 (OUTLIER) cc_final: 0.4905 (pp)
  outliers start: 12
  outliers final: 8
  residues processed: 70
  average time/residue: 0.1424
  time to fit residues: 12.6322
Evaluate side-chains
  68 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  385 THR
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain B residue   64 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    0.1980
   chunk 37 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 10 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 = 0.3861 r_free = 0.3861 target = 0.169493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.138478 restraints weight = 3772.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.142005 restraints weight = 2736.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.144427 restraints weight = 2220.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   3381  Z= 0.148
  Angle     :  0.659  10.456   4612  Z= 0.333
  Chirality :  0.046   0.226    502
  Planarity :  0.005   0.041    591
  Dihedral  :  5.428  26.650    524
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.78 %
    Favored  : 90.22 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.90 %
    Favored  : 79.26 %
  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: -2.35 (0.42), residues: 409
  helix: -3.06 (1.71), residues: 6
  sheet: -1.23 (0.45), residues: 135
  loop : -1.77 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP R 436 
 HIS   0.001   0.000   HIS R 505 
 PHE   0.022   0.002   PHE R 456 
 TYR   0.014   0.001   TYR R 495 
 ARG   0.008   0.001   ARG A  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00190 (    1)
  link_NAG-ASN         : angle       1.08420 (    3)
  link_BETA1-4         : bond        0.00092 (    1)
  link_BETA1-4         : angle       1.32907 (    3)
  hydrogen bonds       : bond        0.03187 (   74)
  hydrogen bonds       : angle       5.78739 (  174)
  link_BETA1-6         : bond        0.00048 (    1)
  link_BETA1-6         : angle       1.90505 (    3)
  SS BOND              : bond        0.00503 (    5)
  SS BOND              : angle       1.85313 (   10)
  covalent geometry    : bond        0.00357 ( 3373)
  covalent geometry    : angle       0.65181 ( 4593)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.393 
Fit side-chains
REVERT: R  396 TYR cc_start: 0.7766 (m-80) cc_final: 0.7545 (m-80)
REVERT: A  103 LEU cc_start: 0.5262 (OUTLIER) cc_final: 0.4917 (pp)
  outliers start: 10
  outliers final: 9
  residues processed: 72
  average time/residue: 0.1398
  time to fit residues: 12.7351
Evaluate side-chains
  72 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  385 THR
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue   76 THR
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue   71 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0470
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0060
   chunk 4 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0170
   chunk 0 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0470
   overall best weight:    0.1430

-------------------------------------------------------------------------------
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 = 0.3917 r_free = 0.3917 target = 0.174262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.146789 restraints weight = 3734.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.150429 restraints weight = 2623.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.153011 restraints weight = 2059.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.2898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3381  Z= 0.116
  Angle     :  0.632   8.803   4612  Z= 0.320
  Chirality :  0.045   0.174    502
  Planarity :  0.005   0.050    591
  Dihedral  :  5.292  23.808    524
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 19.32 %
    Favored  : 78.69 %
  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: -2.23 (0.42), residues: 409
  helix: -2.56 (1.88), residues: 6
  sheet: -0.84 (0.47), residues: 131
  loop : -1.88 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP R 436 
 HIS   0.001   0.000   HIS B  97 
 PHE   0.026   0.002   PHE R 456 
 TYR   0.010   0.001   TYR R 495 
 ARG   0.008   0.001   ARG A  87 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00168 (    1)
  link_NAG-ASN         : angle       0.60166 (    3)
  link_BETA1-4         : bond        0.00233 (    1)
  link_BETA1-4         : angle       0.94448 (    3)
  hydrogen bonds       : bond        0.02956 (   74)
  hydrogen bonds       : angle       5.65197 (  174)
  link_BETA1-6         : bond        0.00145 (    1)
  link_BETA1-6         : angle       1.49624 (    3)
  SS BOND              : bond        0.00716 (    5)
  SS BOND              : angle       1.97119 (   10)
  covalent geometry    : bond        0.00275 ( 3373)
  covalent geometry    : angle       0.62439 ( 4593)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2314.20 seconds
wall clock time: 43 minutes 40.65 seconds (2620.65 seconds total)