Starting phenix.real_space_refine
on Fri May  9 17:48:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y6n_33644/05_2025/7y6n_33644.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y6n_33644/05_2025/7y6n_33644.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y6n_33644/05_2025/7y6n_33644.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y6n_33644/05_2025/7y6n_33644.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y6n_33644/05_2025/7y6n_33644.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y6n_33644/05_2025/7y6n_33644.cif"
  }
  resolution = 4.4
  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=   0.004
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    2112      2.51       5
     N     565      2.21       5
     O     635      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3327
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1568
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 11, 'TRANS': 186}
    Chain: "H"
      Number of atoms: 948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 948
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 4, 'TRANS': 117}
    Chain: "L"
      Number of atoms: 797
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 797
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.57, per 1000 atoms: 0.77
  Number of scatterers: 3327
  At special positions: 0
  Unit cell: (65.491, 60.517, 107.77, 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     635      8.00
     N     565      7.00
     C    2112      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 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  23 " - pdb=" SG  CYS L  88 " distance=2.04

  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
    NAG-ASN
      " NAG A1301 " - " ASN A 343 "
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 370.3 milliseconds
  

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  778

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 6 sheets defined
      9.9% alpha, 25.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 364 through 371
      removed outlier: 3.916A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 390
      removed outlier: 3.965A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 3.909A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.933A  pdb=" N   PHE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 453
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.496A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   GLY H  50 " --> pdb=" O   ALA H  59 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ALA H  59 " --> pdb=" O   GLY H  50 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.500A  pdb=" N   LEU L  11 " --> pdb=" O   LYS L 103 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   GLN L  37 " --> pdb=" O   LEU L  46 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   LEU L  46 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)

    100 hydrogen bonds defined for protein.
    228 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.83

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1069
        1.34 -     1.47: 901
        1.47 -     1.59: 1424
        1.59 -     1.71: 0
        1.71 -     1.83: 17
  Bond restraints: 3411
  Sorted by residual:
  bond pdb=" C1  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.13e+00
  bond pdb=" C5  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.35e+00
  bond pdb=" CB  LYS A 462 "
       pdb=" CG  LYS A 462 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.10e+00
  bond pdb=" N   ASN H  77 "
       pdb=" CA  ASN H  77 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.013 1.29e-02 6.01e+03 1.07e+00
  bond pdb=" C3  NAG A1301 "
       pdb=" O3  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 1.03e+00
  ... (remaining 3406 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 4365
        1.54 -     3.09: 214
        3.09 -     4.63: 38
        4.63 -     6.18: 10
        6.18 -     7.72: 8
  Bond angle restraints: 4635
  Sorted by residual:
  angle pdb=" C   PRO A 479 "
        pdb=" N   CYS A 480 "
        pdb=" CA  CYS A 480 "
      ideal   model   delta    sigma   weight residual
     121.94  114.95    6.99 2.00e+00 2.50e-01 1.22e+01
  angle pdb=" N   PHE A 338 "
        pdb=" CA  PHE A 338 "
        pdb=" C   PHE A 338 "
      ideal   model   delta    sigma   weight residual
     114.56  110.18    4.38 1.27e+00 6.20e-01 1.19e+01
  angle pdb=" CB  LYS A 462 "
        pdb=" CG  LYS A 462 "
        pdb=" CD  LYS A 462 "
      ideal   model   delta    sigma   weight residual
     111.30  118.99   -7.69 2.30e+00 1.89e-01 1.12e+01
  angle pdb=" N   GLY L  41 "
        pdb=" CA  GLY L  41 "
        pdb=" C   GLY L  41 "
      ideal   model   delta    sigma   weight residual
     113.58  116.85   -3.27 1.07e+00 8.73e-01 9.33e+00
  angle pdb=" N   PHE L  92 "
        pdb=" CA  PHE L  92 "
        pdb=" C   PHE L  92 "
      ideal   model   delta    sigma   weight residual
     109.96  105.46    4.50 1.58e+00 4.01e-01 8.10e+00
  ... (remaining 4630 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.24: 1799
       16.24 -    32.47: 176
       32.47 -    48.71: 30
       48.71 -    64.94: 14
       64.94 -    81.18: 3
  Dihedral angle restraints: 2022
    sinusoidal: 796
      harmonic: 1226
  Sorted by residual:
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   11.82   81.18     1      1.00e+01 1.00e-02 8.13e+01
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  155.64  -62.64     1      1.00e+01 1.00e-02 5.19e+01
  dihedral pdb=" CB  CYS A 336 "
           pdb=" SG  CYS A 336 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -147.95   61.95     1      1.00e+01 1.00e-02 5.09e+01
  ... (remaining 2019 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 356
       0.046 -    0.091: 106
       0.091 -    0.137: 34
       0.137 -    0.182: 4
       0.182 -    0.228: 1
  Chirality restraints: 501
  Sorted by residual:
  chirality pdb=" C1  NAG A1301 "
            pdb=" ND2 ASN A 343 "
            pdb=" C2  NAG A1301 "
            pdb=" O5  NAG A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CA  THR L  94 "
            pdb=" N   THR L  94 "
            pdb=" C   THR L  94 "
            pdb=" CB  THR L  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.17 2.00e-01 2.50e+01 7.46e-01
  chirality pdb=" CA  ILE A 434 "
            pdb=" N   ILE A 434 "
            pdb=" C   ILE A 434 "
            pdb=" CB  ILE A 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.78e-01
  ... (remaining 498 not shown)

  Planarity restraints: 602
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 490 "    0.070 5.00e-02 4.00e+02   1.08e-01 1.88e+01
        pdb=" N   PRO A 491 "   -0.188 5.00e-02 4.00e+02
        pdb=" CA  PRO A 491 "    0.060 5.00e-02 4.00e+02
        pdb=" CD  PRO A 491 "    0.058 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  36 "   -0.012 2.00e-02 2.50e+03   9.63e-03 2.32e+00
        pdb=" CG  TRP H  36 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  36 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  36 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  36 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  36 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  36 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  36 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  36 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL L  58 "   -0.022 5.00e-02 4.00e+02   3.32e-02 1.76e+00
        pdb=" N   PRO L  59 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO L  59 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO L  59 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 599 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 507
        2.76 -     3.29: 3418
        3.29 -     3.83: 5417
        3.83 -     4.36: 6147
        4.36 -     4.90: 10455
  Nonbonded interactions: 25944
  Sorted by model distance:
  nonbonded pdb=" O   GLY H  85 "
            pdb=" NH1 ARG H  87 "
     model   vdw
     2.222 3.120
  nonbonded pdb=" OG  SER L  14 "
            pdb=" O   LYS L 107 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OH  TYR H 102 "
            pdb=" NE2 GLN L  55 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" O   PRO L   8 "
            pdb=" OG1 THR L 102 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OD1 ASN A 354 "
            pdb=" N   ARG A 355 "
     model   vdw
     2.302 3.120
  ... (remaining 25939 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:             0.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.230
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5575
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   0.035   3418  Z= 0.157
  Angle     :  0.855   7.724   4650  Z= 0.449
  Chirality :  0.047   0.228    501
  Planarity :  0.006   0.108    601
  Dihedral  : 12.983  81.022   1226
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.14 %
    Favored  : 87.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.77 (0.39), residues: 420
  helix: -2.48 (0.92), residues: 28
  sheet: -1.35 (0.43), residues: 138
  loop : -2.10 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP H  36 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.021   0.001   PHE L  92 
 TYR   0.009   0.001   TYR A 365 
 ARG   0.003   0.000   ARG H  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01563 (    1)
  link_NAG-ASN         : angle       4.67945 (    3)
  hydrogen bonds       : bond        0.15178 (  100)
  hydrogen bonds       : angle       8.66608 (  228)
  SS BOND              : bond        0.00496 (    6)
  SS BOND              : angle       2.78045 (   12)
  covalent geometry    : bond        0.00324 ( 3411)
  covalent geometry    : angle       0.83660 ( 4635)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 LEU cc_start: 0.5807 (tt) cc_final: 0.5411 (tp)
REVERT: A  417 LYS cc_start: 0.6909 (ptmt) cc_final: 0.6335 (tppt)
REVERT: A  424 LYS cc_start: 0.7203 (tmmt) cc_final: 0.6589 (tptt)
REVERT: A  436 TRP cc_start: 0.6532 (p90) cc_final: 0.5933 (p90)
REVERT: A  439 ASN cc_start: 0.6843 (t0) cc_final: 0.6558 (t0)
REVERT: A  453 TYR cc_start: 0.6462 (p90) cc_final: 0.5882 (p90)
REVERT: A  461 LEU cc_start: 0.6388 (mm) cc_final: 0.6047 (mm)
REVERT: A  466 ARG cc_start: 0.7581 (mtp85) cc_final: 0.7368 (ttm170)
REVERT: A  489 TYR cc_start: 0.7858 (m-10) cc_final: 0.7087 (m-10)
REVERT: H   78 SER cc_start: 0.7214 (t) cc_final: 0.6535 (m)
REVERT: H   90 ASP cc_start: 0.4947 (m-30) cc_final: 0.4626 (m-30)
REVERT: H  101 ARG cc_start: 0.7298 (tpt170) cc_final: 0.5685 (ttm170)
REVERT: L   92 PHE cc_start: 0.5994 (t80) cc_final: 0.5333 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1663
  time to fit residues: 21.2115
Evaluate side-chains
  77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:   20.0000
   chunk 31 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   chunk 10 optimal weight:    0.3980
   chunk 20 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0770
   chunk 32 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 19 optimal weight:   20.0000
   chunk 23 optimal weight:    8.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    1.8742

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

Flipped N/Q/H residues before XYZ refinement:
L  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.166485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.140171 restraints weight = 5679.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.143711 restraints weight = 3626.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.146256 restraints weight = 2609.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6327
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3418  Z= 0.143
  Angle     :  0.765   6.281   4650  Z= 0.390
  Chirality :  0.047   0.189    501
  Planarity :  0.006   0.072    601
  Dihedral  :  5.948  25.480    491
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.95 %
    Favored  : 89.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.64 (0.40), residues: 420
  helix: -2.06 (0.98), residues: 27
  sheet: -1.55 (0.40), residues: 150
  loop : -1.86 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP L  35 
 HIS   0.003   0.002   HIS H  35 
 PHE   0.014   0.002   PHE A 497 
 TYR   0.011   0.002   TYR L  49 
 ARG   0.004   0.001   ARG A 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01490 (    1)
  link_NAG-ASN         : angle       4.54220 (    3)
  hydrogen bonds       : bond        0.03452 (  100)
  hydrogen bonds       : angle       7.15888 (  228)
  SS BOND              : bond        0.00468 (    6)
  SS BOND              : angle       3.03659 (   12)
  covalent geometry    : bond        0.00321 ( 3411)
  covalent geometry    : angle       0.74131 ( 4635)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: A  368 LEU cc_start: 0.7101 (mm) cc_final: 0.6859 (mt)
REVERT: A  387 LEU cc_start: 0.6748 (tt) cc_final: 0.6266 (tp)
REVERT: A  417 LYS cc_start: 0.7456 (ptmt) cc_final: 0.7034 (tppt)
REVERT: A  436 TRP cc_start: 0.7158 (p90) cc_final: 0.6899 (p90)
REVERT: A  453 TYR cc_start: 0.7489 (p90) cc_final: 0.7062 (p90)
REVERT: H   29 PHE cc_start: 0.5976 (t80) cc_final: 0.5765 (t80)
REVERT: H   78 SER cc_start: 0.6865 (t) cc_final: 0.6338 (m)
REVERT: H  101 ARG cc_start: 0.7237 (tpt170) cc_final: 0.6345 (ttm170)
REVERT: L   22 THR cc_start: 0.6429 (p) cc_final: 0.6063 (m)
REVERT: L   92 PHE cc_start: 0.6254 (t80) cc_final: 0.5634 (t80)
REVERT: L  102 THR cc_start: 0.6396 (t) cc_final: 0.5885 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1483
  time to fit residues: 15.1224
Evaluate side-chains
  72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 34 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 17 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 26 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
L  34 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.160049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.135872 restraints weight = 5781.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.139077 restraints weight = 3739.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.141435 restraints weight = 2714.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6471
moved from start:          0.3363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.084   3418  Z= 0.231
  Angle     :  0.905   8.077   4650  Z= 0.465
  Chirality :  0.052   0.212    501
  Planarity :  0.006   0.047    601
  Dihedral  :  7.303  43.236    491
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.81 %
    Favored  : 86.19 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  6.94 %
    Favored  : 92.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.81 (0.41), residues: 420
  helix: -2.25 (0.98), residues: 27
  sheet: -1.82 (0.41), residues: 143
  loop : -1.86 (0.42), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP L  35 
 HIS   0.006   0.004   HIS H  35 
 PHE   0.016   0.002   PHE A 497 
 TYR   0.017   0.003   TYR L  49 
 ARG   0.004   0.001   ARG A 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01698 (    1)
  link_NAG-ASN         : angle       4.19924 (    3)
  hydrogen bonds       : bond        0.04219 (  100)
  hydrogen bonds       : angle       7.55214 (  228)
  SS BOND              : bond        0.00575 (    6)
  SS BOND              : angle       4.15185 (   12)
  covalent geometry    : bond        0.00529 ( 3411)
  covalent geometry    : angle       0.87536 ( 4635)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: A  368 LEU cc_start: 0.7245 (mm) cc_final: 0.6762 (mt)
REVERT: A  387 LEU cc_start: 0.6784 (tt) cc_final: 0.6542 (tp)
REVERT: A  417 LYS cc_start: 0.7798 (ptmt) cc_final: 0.7171 (tppt)
REVERT: A  439 ASN cc_start: 0.8285 (t0) cc_final: 0.7980 (t0)
REVERT: A  462 LYS cc_start: 0.8410 (tppt) cc_final: 0.7627 (ptmt)
REVERT: H   13 GLN cc_start: 0.6999 (mm-40) cc_final: 0.6583 (pm20)
REVERT: H   72 ARG cc_start: 0.5677 (ttt90) cc_final: 0.5361 (ttt90)
REVERT: H   78 SER cc_start: 0.6639 (t) cc_final: 0.6368 (m)
REVERT: H   93 LEU cc_start: 0.6986 (mt) cc_final: 0.6663 (mt)
REVERT: H  113 PHE cc_start: 0.7470 (m-80) cc_final: 0.7114 (m-80)
REVERT: L   92 PHE cc_start: 0.6216 (t80) cc_final: 0.5584 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1627
  time to fit residues: 17.1536
Evaluate side-chains
  76 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 7 optimal weight:    0.3980
   chunk 16 optimal weight:    0.2980
   chunk 2 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
L  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.166494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.141758 restraints weight = 5752.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.145303 restraints weight = 3653.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.147783 restraints weight = 2606.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6313
moved from start:          0.3421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3418  Z= 0.118
  Angle     :  0.741   6.774   4650  Z= 0.376
  Chirality :  0.046   0.199    501
  Planarity :  0.005   0.043    601
  Dihedral  :  5.916  24.798    491
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.67 %
    Favored  : 88.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.66 (0.41), residues: 420
  helix: -2.37 (0.98), residues: 27
  sheet: -1.70 (0.40), residues: 149
  loop : -1.71 (0.42), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP H 114 
 HIS   0.001   0.001   HIS H  35 
 PHE   0.013   0.002   PHE H  29 
 TYR   0.012   0.001   TYR A 453 
 ARG   0.003   0.000   ARG A 355 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01319 (    1)
  link_NAG-ASN         : angle       4.25655 (    3)
  hydrogen bonds       : bond        0.03043 (  100)
  hydrogen bonds       : angle       7.04833 (  228)
  SS BOND              : bond        0.00528 (    6)
  SS BOND              : angle       2.93709 (   12)
  covalent geometry    : bond        0.00249 ( 3411)
  covalent geometry    : angle       0.71908 ( 4635)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: A  368 LEU cc_start: 0.7191 (mm) cc_final: 0.6811 (mt)
REVERT: A  417 LYS cc_start: 0.7475 (ptmt) cc_final: 0.7199 (tppt)
REVERT: A  461 LEU cc_start: 0.6835 (mm) cc_final: 0.6586 (mm)
REVERT: A  462 LYS cc_start: 0.8355 (tppt) cc_final: 0.7888 (pttm)
REVERT: H   13 GLN cc_start: 0.6995 (mm-40) cc_final: 0.6646 (pm20)
REVERT: H   29 PHE cc_start: 0.5691 (t80) cc_final: 0.5241 (t80)
REVERT: H   72 ARG cc_start: 0.5272 (ttt90) cc_final: 0.4863 (tpt-90)
REVERT: H   93 LEU cc_start: 0.7076 (mt) cc_final: 0.6868 (mt)
REVERT: H  101 ARG cc_start: 0.7058 (tpt170) cc_final: 0.6374 (ttp-170)
REVERT: H  113 PHE cc_start: 0.7348 (m-80) cc_final: 0.6989 (m-80)
REVERT: L   92 PHE cc_start: 0.5979 (t80) cc_final: 0.5262 (t80)
REVERT: L  102 THR cc_start: 0.6182 (t) cc_final: 0.5638 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1846
  time to fit residues: 17.9051
Evaluate side-chains
  67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 26 optimal weight:    8.9990
   chunk 40 optimal weight:    0.2980
   chunk 16 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 2 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 25 optimal weight:    9.9990
   overall best weight:    3.2588

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

Flipped N/Q/H residues before XYZ refinement:
A 439 ASN
L  34 ASN

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 = 0.162853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.138223 restraints weight = 5862.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.141590 restraints weight = 3779.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.144072 restraints weight = 2748.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6444
moved from start:          0.4061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   3418  Z= 0.205
  Angle     :  0.864   7.633   4650  Z= 0.444
  Chirality :  0.050   0.222    501
  Planarity :  0.006   0.049    601
  Dihedral  :  6.939  35.784    491
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.33 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  5.00 %
    Favored  : 94.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.83 (0.41), residues: 420
  helix: -2.37 (0.97), residues: 27
  sheet: -1.83 (0.41), residues: 143
  loop : -1.86 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP L  35 
 HIS   0.004   0.002   HIS H  35 
 PHE   0.023   0.002   PHE L  71 
 TYR   0.017   0.002   TYR A 453 
 ARG   0.007   0.001   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01480 (    1)
  link_NAG-ASN         : angle       3.96990 (    3)
  hydrogen bonds       : bond        0.04094 (  100)
  hydrogen bonds       : angle       7.31261 (  228)
  SS BOND              : bond        0.00686 (    6)
  SS BOND              : angle       4.15071 (   12)
  covalent geometry    : bond        0.00471 ( 3411)
  covalent geometry    : angle       0.83311 ( 4635)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  403 ARG cc_start: 0.6005 (mtm110) cc_final: 0.5633 (mtm110)
REVERT: A  417 LYS cc_start: 0.7631 (ptmt) cc_final: 0.7331 (tppt)
REVERT: A  461 LEU cc_start: 0.6550 (mm) cc_final: 0.6307 (mm)
REVERT: A  462 LYS cc_start: 0.8389 (tppt) cc_final: 0.7707 (ptmt)
REVERT: H   13 GLN cc_start: 0.7004 (mm-40) cc_final: 0.6553 (pm20)
REVERT: H   29 PHE cc_start: 0.5925 (t80) cc_final: 0.5645 (t80)
REVERT: H   93 LEU cc_start: 0.7002 (mt) cc_final: 0.6765 (mt)
REVERT: H  113 PHE cc_start: 0.7318 (m-80) cc_final: 0.7065 (m-80)
REVERT: L   92 PHE cc_start: 0.6115 (t80) cc_final: 0.5357 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 86
  average time/residue: 0.1497
  time to fit residues: 15.7900
Evaluate side-chains
  74 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0970
   chunk 20 optimal weight:    0.3980
   chunk 34 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 32 optimal weight:   20.0000
   chunk 24 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 39 optimal weight:    5.9990
   chunk 9 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:
** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 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 = 0.3936 r_free = 0.3936 target = 0.167028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.142465 restraints weight = 5819.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.146032 restraints weight = 3627.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.148621 restraints weight = 2575.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6324
moved from start:          0.4165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3418  Z= 0.123
  Angle     :  0.757   8.521   4650  Z= 0.385
  Chirality :  0.047   0.177    501
  Planarity :  0.005   0.042    601
  Dihedral  :  5.991  26.123    491
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.19 %
    Favored  : 88.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 (0.41), residues: 420
  helix: -2.21 (1.02), residues: 27
  sheet: -1.53 (0.41), residues: 147
  loop : -1.73 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP L  35 
 HIS   0.001   0.001   HIS H  35 
 PHE   0.013   0.002   PHE A 429 
 TYR   0.013   0.001   TYR A 453 
 ARG   0.004   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01288 (    1)
  link_NAG-ASN         : angle       4.03710 (    3)
  hydrogen bonds       : bond        0.03192 (  100)
  hydrogen bonds       : angle       6.90607 (  228)
  SS BOND              : bond        0.00788 (    6)
  SS BOND              : angle       2.98678 (   12)
  covalent geometry    : bond        0.00258 ( 3411)
  covalent geometry    : angle       0.73588 ( 4635)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: A  368 LEU cc_start: 0.7234 (mm) cc_final: 0.6830 (mt)
REVERT: A  393 THR cc_start: 0.6655 (m) cc_final: 0.6297 (p)
REVERT: A  403 ARG cc_start: 0.5877 (mtm110) cc_final: 0.5517 (mtm110)
REVERT: A  442 ASP cc_start: 0.5339 (m-30) cc_final: 0.4871 (t0)
REVERT: A  461 LEU cc_start: 0.6716 (mm) cc_final: 0.6428 (mm)
REVERT: A  462 LYS cc_start: 0.8419 (tppt) cc_final: 0.7969 (pttm)
REVERT: H   13 GLN cc_start: 0.7049 (mm-40) cc_final: 0.6579 (pm20)
REVERT: H   29 PHE cc_start: 0.5754 (t80) cc_final: 0.5172 (t80)
REVERT: L   37 GLN cc_start: 0.5830 (pp30) cc_final: 0.5522 (pp30)
REVERT: L   92 PHE cc_start: 0.6004 (t80) cc_final: 0.5084 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1482
  time to fit residues: 15.4163
Evaluate side-chains
  72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 24 optimal weight:    0.0770
   chunk 29 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   chunk 37 optimal weight:   20.0000
   chunk 14 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0970
   chunk 34 optimal weight:    0.0040
   overall best weight:    0.6350

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

Flipped N/Q/H residues before XYZ refinement:
** L  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 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 = 0.3963 r_free = 0.3963 target = 0.169447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.144795 restraints weight = 5688.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.148252 restraints weight = 3616.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.150757 restraints weight = 2605.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6296
moved from start:          0.4292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3418  Z= 0.113
  Angle     :  0.729   8.671   4650  Z= 0.366
  Chirality :  0.045   0.188    501
  Planarity :  0.004   0.039    601
  Dihedral  :  5.784  25.385    491
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.14 %
    Favored  : 87.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: 420
  helix: -2.25 (1.02), residues: 27
  sheet: -1.41 (0.41), residues: 147
  loop : -1.64 (0.43), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP L  35 
 HIS   0.001   0.000   HIS H  35 
 PHE   0.011   0.002   PHE L  62 
 TYR   0.014   0.001   TYR A 453 
 ARG   0.004   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01292 (    1)
  link_NAG-ASN         : angle       4.15682 (    3)
  hydrogen bonds       : bond        0.02934 (  100)
  hydrogen bonds       : angle       6.75783 (  228)
  SS BOND              : bond        0.00476 (    6)
  SS BOND              : angle       2.86297 (   12)
  covalent geometry    : bond        0.00240 ( 3411)
  covalent geometry    : angle       0.70765 ( 4635)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A  368 LEU cc_start: 0.7288 (mm) cc_final: 0.6887 (mt)
REVERT: A  386 LYS cc_start: 0.5439 (pptt) cc_final: 0.4495 (ptmt)
REVERT: A  393 THR cc_start: 0.6633 (m) cc_final: 0.6239 (p)
REVERT: A  425 LEU cc_start: 0.8130 (mp) cc_final: 0.7787 (mp)
REVERT: A  442 ASP cc_start: 0.5334 (m-30) cc_final: 0.4920 (t0)
REVERT: A  461 LEU cc_start: 0.6579 (mm) cc_final: 0.6248 (mm)
REVERT: A  462 LYS cc_start: 0.8410 (tppt) cc_final: 0.7955 (pttm)
REVERT: H   13 GLN cc_start: 0.7081 (mm-40) cc_final: 0.6577 (pm20)
REVERT: H   29 PHE cc_start: 0.5665 (t80) cc_final: 0.5460 (t80)
REVERT: H  111 PHE cc_start: 0.8356 (m-10) cc_final: 0.8075 (m-10)
REVERT: H  122 VAL cc_start: 0.5084 (t) cc_final: 0.4810 (t)
REVERT: L   37 GLN cc_start: 0.5974 (pp30) cc_final: 0.5605 (pp30)
REVERT: L   92 PHE cc_start: 0.6005 (t80) cc_final: 0.5051 (t80)
REVERT: L   93 THR cc_start: 0.6891 (p) cc_final: 0.6615 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1464
  time to fit residues: 14.7601
Evaluate side-chains
  72 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0040
   chunk 3 optimal weight:    9.9990
   chunk 10 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 28 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
L  34 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.170083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.145459 restraints weight = 5786.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.149040 restraints weight = 3677.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.151624 restraints weight = 2628.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6258
moved from start:          0.4346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3418  Z= 0.110
  Angle     :  0.712   7.756   4650  Z= 0.357
  Chirality :  0.045   0.185    501
  Planarity :  0.004   0.039    601
  Dihedral  :  5.609  24.452    491
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.19 %
    Favored  : 88.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.36 (0.42), residues: 420
  helix: -2.36 (0.98), residues: 27
  sheet: -1.35 (0.43), residues: 146
  loop : -1.60 (0.42), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP L  35 
 HIS   0.001   0.000   HIS H  35 
 PHE   0.016   0.001   PHE A 429 
 TYR   0.013   0.001   TYR A 453 
 ARG   0.003   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01256 (    1)
  link_NAG-ASN         : angle       4.29808 (    3)
  hydrogen bonds       : bond        0.03032 (  100)
  hydrogen bonds       : angle       6.59643 (  228)
  SS BOND              : bond        0.00431 (    6)
  SS BOND              : angle       2.91679 (   12)
  covalent geometry    : bond        0.00238 ( 3411)
  covalent geometry    : angle       0.68938 ( 4635)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  368 LEU cc_start: 0.7271 (mm) cc_final: 0.6893 (mt)
REVERT: A  393 THR cc_start: 0.6625 (m) cc_final: 0.6312 (p)
REVERT: A  425 LEU cc_start: 0.7962 (mp) cc_final: 0.7751 (mp)
REVERT: A  442 ASP cc_start: 0.5483 (m-30) cc_final: 0.5047 (t0)
REVERT: A  461 LEU cc_start: 0.6567 (mm) cc_final: 0.6263 (mm)
REVERT: A  462 LYS cc_start: 0.8444 (tppt) cc_final: 0.7984 (pttm)
REVERT: H   13 GLN cc_start: 0.7090 (mm-40) cc_final: 0.6507 (pm20)
REVERT: H   72 ARG cc_start: 0.5023 (ttt90) cc_final: 0.4660 (ttt90)
REVERT: H  111 PHE cc_start: 0.8385 (m-10) cc_final: 0.8089 (m-10)
REVERT: L   92 PHE cc_start: 0.6025 (t80) cc_final: 0.5106 (t80)
REVERT: L   93 THR cc_start: 0.6947 (p) cc_final: 0.6734 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1520
  time to fit residues: 14.6232
Evaluate side-chains
  70 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 19 optimal weight:   20.0000
   chunk 24 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   chunk 11 optimal weight:    0.0770
   chunk 3 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 29 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.6540

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

Flipped N/Q/H residues before XYZ refinement:
H  82 GLN
L  34 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.172102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.147329 restraints weight = 5614.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.150921 restraints weight = 3585.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.153453 restraints weight = 2565.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6224
moved from start:          0.4491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   3418  Z= 0.113
  Angle     :  0.717   7.457   4650  Z= 0.356
  Chirality :  0.046   0.190    501
  Planarity :  0.004   0.037    601
  Dihedral  :  5.569  25.660    491
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.95 %
    Favored  : 89.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.30 (0.42), residues: 420
  helix: -2.39 (0.98), residues: 27
  sheet: -1.15 (0.44), residues: 143
  loop : -1.67 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP L  35 
 HIS   0.001   0.000   HIS H  35 
 PHE   0.010   0.001   PHE A 515 
 TYR   0.013   0.001   TYR A 453 
 ARG   0.003   0.000   ARG A 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01308 (    1)
  link_NAG-ASN         : angle       4.20864 (    3)
  hydrogen bonds       : bond        0.02965 (  100)
  hydrogen bonds       : angle       6.42631 (  228)
  SS BOND              : bond        0.00429 (    6)
  SS BOND              : angle       2.88000 (   12)
  covalent geometry    : bond        0.00243 ( 3411)
  covalent geometry    : angle       0.69486 ( 4635)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: A  368 LEU cc_start: 0.7221 (mm) cc_final: 0.6832 (mt)
REVERT: A  393 THR cc_start: 0.6632 (m) cc_final: 0.6297 (p)
REVERT: A  410 ILE cc_start: 0.7790 (mm) cc_final: 0.7317 (pt)
REVERT: A  442 ASP cc_start: 0.5412 (m-30) cc_final: 0.4978 (t0)
REVERT: A  461 LEU cc_start: 0.6578 (mm) cc_final: 0.6193 (mm)
REVERT: A  462 LYS cc_start: 0.8451 (tppt) cc_final: 0.7982 (pttm)
REVERT: H   13 GLN cc_start: 0.7086 (mm-40) cc_final: 0.6481 (pm20)
REVERT: H  101 ARG cc_start: 0.7127 (tpt170) cc_final: 0.6000 (tmm-80)
REVERT: H  111 PHE cc_start: 0.8332 (m-10) cc_final: 0.8113 (m-10)
REVERT: L   92 PHE cc_start: 0.6135 (t80) cc_final: 0.5304 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1438
  time to fit residues: 13.7126
Evaluate side-chains
  63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 13 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9980
   chunk 18 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  34 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.166718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.143290 restraints weight = 5676.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.146658 restraints weight = 3639.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.149108 restraints weight = 2614.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6349
moved from start:          0.4755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3418  Z= 0.160
  Angle     :  0.800   7.941   4650  Z= 0.405
  Chirality :  0.048   0.167    501
  Planarity :  0.005   0.050    601
  Dihedral  :  6.325  26.976    491
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.90 %
    Favored  : 88.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.53 (0.42), residues: 420
  helix: -2.54 (0.94), residues: 27
  sheet: -1.37 (0.43), residues: 141
  loop : -1.78 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP L  35 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.012   0.002   PHE A 429 
 TYR   0.020   0.002   TYR A 453 
 ARG   0.003   0.000   ARG H 101 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01305 (    1)
  link_NAG-ASN         : angle       3.83453 (    3)
  hydrogen bonds       : bond        0.03440 (  100)
  hydrogen bonds       : angle       6.73861 (  228)
  SS BOND              : bond        0.00466 (    6)
  SS BOND              : angle       3.65443 (   12)
  covalent geometry    : bond        0.00364 ( 3411)
  covalent geometry    : angle       0.77315 ( 4635)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
REVERT: A  368 LEU cc_start: 0.7344 (mm) cc_final: 0.6876 (mt)
REVERT: A  393 THR cc_start: 0.6691 (m) cc_final: 0.6318 (p)
REVERT: A  442 ASP cc_start: 0.5604 (m-30) cc_final: 0.5002 (t0)
REVERT: A  461 LEU cc_start: 0.6418 (mm) cc_final: 0.6055 (mm)
REVERT: A  462 LYS cc_start: 0.8441 (tppt) cc_final: 0.7975 (pttm)
REVERT: H   13 GLN cc_start: 0.7028 (mm-40) cc_final: 0.6477 (pm20)
REVERT: H  111 PHE cc_start: 0.8408 (m-10) cc_final: 0.8195 (m-10)
REVERT: L   92 PHE cc_start: 0.6211 (t80) cc_final: 0.5388 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1460
  time to fit residues: 14.0131
Evaluate side-chains
  64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 25 optimal weight:    0.0170
   chunk 37 optimal weight:    9.9990
   chunk 29 optimal weight:    4.9990
   chunk 32 optimal weight:    9.9990
   chunk 0 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    2.8026

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

Flipped N/Q/H residues before XYZ refinement:
** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 474 GLN
H  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.165959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.142606 restraints weight = 5750.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.145920 restraints weight = 3692.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.148331 restraints weight = 2680.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6393
moved from start:          0.5067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3418  Z= 0.172
  Angle     :  0.823   7.745   4650  Z= 0.418
  Chirality :  0.048   0.166    501
  Planarity :  0.005   0.046    601
  Dihedral  :  6.507  27.576    491
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.43 %
    Favored  : 88.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -2.67 (0.41), residues: 420
  helix: -2.72 (0.89), residues: 27
  sheet: -1.46 (0.43), residues: 139
  loop : -1.87 (0.41), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP L  35 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.019   0.002   PHE H 113 
 TYR   0.022   0.002   TYR A 453 
 ARG   0.011   0.001   ARG H 101 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01226 (    1)
  link_NAG-ASN         : angle       3.72095 (    3)
  hydrogen bonds       : bond        0.03548 (  100)
  hydrogen bonds       : angle       6.91875 (  228)
  SS BOND              : bond        0.00483 (    6)
  SS BOND              : angle       3.86165 (   12)
  covalent geometry    : bond        0.00388 ( 3411)
  covalent geometry    : angle       0.79449 ( 4635)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1437.93 seconds
wall clock time: 26 minutes 11.41 seconds (1571.41 seconds total)