Starting phenix.real_space_refine
on Tue Mar  3 11:32:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y6n_33644/03_2026/7y6n_33644.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y6n_33644/03_2026/7y6n_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y6n_33644/03_2026/7y6n_33644.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y6n_33644/03_2026/7y6n_33644.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y6n_33644/03_2026/7y6n_33644.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y6n_33644/03_2026/7y6n_33644.map"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.88, per 1000 atoms: 0.26
  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: 0.21
  Conformation dependent library (CDL) restraints added in 128.2 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: 0.12
  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: 0.64

  Time building geometry restraints manager: 0.29 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:             0.330
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.290
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.140
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.003   0.000   ARG H  19 
 TYR   0.009   0.001   TYR A 365 
 PHE   0.021   0.001   PHE L  92 
 TRP   0.026   0.002   TRP H  36 
 HIS   0.003   0.001   HIS H  35 

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

*********************** 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  : 0.179 
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: 0.5883 (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: 0.7297 (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: 0.0631
  time to fit residues: 8.0886
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  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0470
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:   20.0000
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0000
   overall best weight:    3.2088

-------------------------------------------------------------------------------
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 = 0.3867 r_free = 0.3867 target = 0.162134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.136065 restraints weight = 5784.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.139546 restraints weight = 3728.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.142026 restraints weight = 2706.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.143647 restraints weight = 2129.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.144960 restraints weight = 1790.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6393
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3418  Z= 0.196
  Angle     :  0.842   7.597   4650  Z= 0.435
  Chirality :  0.049   0.177    501
  Planarity :  0.006   0.070    601
  Dihedral  :  6.688  33.536    491
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.67 %
    Favored  : 88.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.83 (0.40), residues: 420
  helix: -2.09 (0.99), residues: 27
  sheet: -1.75 (0.39), residues: 150
  loop : -1.94 (0.41), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H 101 
 TYR   0.014   0.002   TYR L  49 
 PHE   0.016   0.002   PHE A 497 
 TRP   0.021   0.003   TRP L  35 
 HIS   0.005   0.003   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 3411)
  covalent geometry    : angle       0.81565 ( 4635)
  SS BOND              : bond        0.00456 (    6)
  SS BOND              : angle       3.57698 (   12)
  hydrogen bonds       : bond        0.03774 (  100)
  hydrogen bonds       : angle       7.34512 (  228)
  link_NAG-ASN         : bond        0.01595 (    1)
  link_NAG-ASN         : angle       4.56976 (    3)

*********************** 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
  85 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  387 LEU cc_start: 0.6788 (tt) cc_final: 0.6291 (tp)
REVERT: A  417 LYS cc_start: 0.7575 (ptmt) cc_final: 0.7074 (tppt)
REVERT: A  436 TRP cc_start: 0.7228 (p90) cc_final: 0.6832 (p90)
REVERT: A  462 LYS cc_start: 0.8364 (tppt) cc_final: 0.7546 (ptmt)
REVERT: H   29 PHE cc_start: 0.6194 (t80) cc_final: 0.5856 (t80)
REVERT: H   78 SER cc_start: 0.6796 (t) cc_final: 0.6361 (m)
REVERT: H  101 ARG cc_start: 0.7309 (tpt170) cc_final: 0.6323 (ttm170)
REVERT: H  113 PHE cc_start: 0.7522 (m-80) cc_final: 0.7101 (m-80)
REVERT: L   22 THR cc_start: 0.6443 (p) cc_final: 0.6156 (m)
REVERT: L   92 PHE cc_start: 0.6295 (t80) cc_final: 0.5959 (t80)
REVERT: L  102 THR cc_start: 0.6325 (t) cc_final: 0.5791 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.0659
  time to fit residues: 6.8549
Evaluate side-chains
  71 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 20 optimal weight:    0.0470
   chunk 1 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 38 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 16 optimal weight:    0.3980
   chunk 32 optimal weight:    5.9990
   overall best weight:    1.4884

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

Flipped N/Q/H residues before XYZ refinement:
L  34 ASN
L  90 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.166048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.140377 restraints weight = 5878.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.143935 restraints weight = 3831.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.146433 restraints weight = 2769.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.148210 restraints weight = 2175.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.149584 restraints weight = 1810.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6308
moved from start:          0.2824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3418  Z= 0.130
  Angle     :  0.744   6.652   4650  Z= 0.379
  Chirality :  0.047   0.185    501
  Planarity :  0.005   0.035    601
  Dihedral  :  5.991  24.394    491
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.14 %
    Favored  : 87.86 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  4.17 %
    Favored  : 95.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.76 (0.41), residues: 420
  helix: -2.15 (1.02), residues: 27
  sheet: -1.79 (0.40), residues: 150
  loop : -1.80 (0.42), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 355 
 TYR   0.019   0.001   TYR A 365 
 PHE   0.011   0.001   PHE A 497 
 TRP   0.020   0.002   TRP L  35 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 3411)
  covalent geometry    : angle       0.71893 ( 4635)
  SS BOND              : bond        0.00135 (    6)
  SS BOND              : angle       3.19845 (   12)
  hydrogen bonds       : bond        0.03229 (  100)
  hydrogen bonds       : angle       6.99398 (  228)
  link_NAG-ASN         : bond        0.01406 (    1)
  link_NAG-ASN         : angle       4.43358 (    3)

*********************** 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
  81 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.072 
Fit side-chains
   revert: symmetry clash
REVERT: A  387 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6288 (tt)
REVERT: A  417 LYS cc_start: 0.7521 (ptmt) cc_final: 0.7103 (tppt)
REVERT: A  462 LYS cc_start: 0.8351 (tppt) cc_final: 0.7590 (ptmt)
REVERT: H   13 GLN cc_start: 0.7032 (mm-40) cc_final: 0.6631 (pm20)
REVERT: H   29 PHE cc_start: 0.6199 (t80) cc_final: 0.5672 (t80)
REVERT: H   78 SER cc_start: 0.6626 (t) cc_final: 0.6249 (m)
REVERT: H   93 LEU cc_start: 0.7088 (mt) cc_final: 0.6798 (mt)
REVERT: H  101 ARG cc_start: 0.7150 (tpt170) cc_final: 0.6103 (ttm170)
REVERT: H  113 PHE cc_start: 0.7408 (m-80) cc_final: 0.7058 (m-80)
REVERT: L   37 GLN cc_start: 0.6149 (pp30) cc_final: 0.5768 (pp30)
REVERT: L   92 PHE cc_start: 0.6327 (t80) cc_final: 0.5801 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0562
  time to fit residues: 5.6774
Evaluate side-chains
  68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:    8.9990
   chunk 6 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   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 439 ASN
L  34 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.160373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.136478 restraints weight = 5950.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.139643 restraints weight = 3964.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.141895 restraints weight = 2921.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.143452 restraints weight = 2312.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.144660 restraints weight = 1944.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6436
moved from start:          0.3979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   3418  Z= 0.234
  Angle     :  0.907   8.783   4650  Z= 0.468
  Chirality :  0.052   0.240    501
  Planarity :  0.006   0.040    601
  Dihedral  :  7.604  46.220    491
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.05 %
    Favored  : 85.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.91 (0.41), residues: 420
  helix: -2.02 (1.09), residues: 27
  sheet: -1.89 (0.39), residues: 147
  loop : -1.95 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 457 
 TYR   0.028   0.003   TYR A 365 
 PHE   0.015   0.002   PHE A 497 
 TRP   0.032   0.003   TRP L  35 
 HIS   0.006   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00524 ( 3411)
  covalent geometry    : angle       0.87398 ( 4635)
  SS BOND              : bond        0.00479 (    6)
  SS BOND              : angle       4.44835 (   12)
  hydrogen bonds       : bond        0.04346 (  100)
  hydrogen bonds       : angle       7.28517 (  228)
  link_NAG-ASN         : bond        0.01624 (    1)
  link_NAG-ASN         : angle       4.12789 (    3)

*********************** 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
  89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
REVERT: A  359 SER cc_start: 0.8625 (p) cc_final: 0.8421 (p)
REVERT: A  417 LYS cc_start: 0.7708 (ptmt) cc_final: 0.7337 (tppt)
REVERT: A  425 LEU cc_start: 0.8014 (mp) cc_final: 0.7774 (mp)
REVERT: A  461 LEU cc_start: 0.6603 (mm) cc_final: 0.6350 (mm)
REVERT: A  462 LYS cc_start: 0.8362 (tppt) cc_final: 0.7716 (ptmt)
REVERT: H   13 GLN cc_start: 0.6931 (mm-40) cc_final: 0.6632 (pm20)
REVERT: H   29 PHE cc_start: 0.6287 (t80) cc_final: 0.5955 (t80)
REVERT: H   93 LEU cc_start: 0.6978 (mt) cc_final: 0.6547 (mt)
REVERT: H  113 PHE cc_start: 0.7353 (m-80) cc_final: 0.7070 (m-80)
REVERT: L   22 THR cc_start: 0.6303 (p) cc_final: 0.5882 (m)
REVERT: L   92 PHE cc_start: 0.6095 (t80) cc_final: 0.5663 (t80)
REVERT: L  102 THR cc_start: 0.6232 (t) cc_final: 0.5776 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.0657
  time to fit residues: 7.0843
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  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 30 optimal weight:   10.0000
   chunk 20 optimal weight:   50.0000
   chunk 36 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 39 optimal weight:   10.0000
   chunk 24 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    4.3388

-------------------------------------------------------------------------------
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 = 0.3856 r_free = 0.3856 target = 0.160154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.136240 restraints weight = 5879.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.139643 restraints weight = 3767.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.142108 restraints weight = 2720.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.143628 restraints weight = 2125.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.144855 restraints weight = 1784.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6450
moved from start:          0.4540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   3418  Z= 0.239
  Angle     :  0.923   9.519   4650  Z= 0.473
  Chirality :  0.051   0.210    501
  Planarity :  0.005   0.041    601
  Dihedral  :  7.797  49.631    491
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.24 %
    Favored  : 84.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.08 (0.41), residues: 420
  helix: -2.10 (1.21), residues: 20
  sheet: -2.04 (0.38), residues: 147
  loop : -2.07 (0.41), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 466 
 TYR   0.013   0.002   TYR L  49 
 PHE   0.019   0.002   PHE A 497 
 TRP   0.032   0.003   TRP L  35 
 HIS   0.005   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00544 ( 3411)
  covalent geometry    : angle       0.88694 ( 4635)
  SS BOND              : bond        0.00254 (    6)
  SS BOND              : angle       4.65582 (   12)
  hydrogen bonds       : bond        0.03983 (  100)
  hydrogen bonds       : angle       7.38948 (  228)
  link_NAG-ASN         : bond        0.01129 (    1)
  link_NAG-ASN         : angle       4.38031 (    3)

*********************** 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
  85 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A  359 SER cc_start: 0.8629 (p) cc_final: 0.8428 (p)
REVERT: A  417 LYS cc_start: 0.7611 (ptmt) cc_final: 0.7409 (tppt)
REVERT: A  439 ASN cc_start: 0.8265 (t0) cc_final: 0.7917 (t0)
REVERT: A  461 LEU cc_start: 0.6682 (mm) cc_final: 0.6338 (mm)
REVERT: A  462 LYS cc_start: 0.8413 (tppt) cc_final: 0.7804 (ptmt)
REVERT: H   13 GLN cc_start: 0.6983 (mm-40) cc_final: 0.6696 (pm20)
REVERT: H   93 LEU cc_start: 0.7070 (mt) cc_final: 0.6870 (mt)
REVERT: L   39 GLU cc_start: 0.7840 (pp20) cc_final: 0.7168 (tm-30)
REVERT: L   71 PHE cc_start: 0.7041 (m-80) cc_final: 0.6197 (m-80)
REVERT: L   92 PHE cc_start: 0.6321 (t80) cc_final: 0.5587 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.0717
  time to fit residues: 7.2491
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  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 34 optimal weight:    7.9990
   chunk 10 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0030
   chunk 22 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    2.1996

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.163916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.140003 restraints weight = 5772.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.143568 restraints weight = 3639.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.146143 restraints weight = 2579.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.147902 restraints weight = 1974.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.149130 restraints weight = 1606.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6365
moved from start:          0.4713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3418  Z= 0.158
  Angle     :  0.832   9.727   4650  Z= 0.423
  Chirality :  0.049   0.174    501
  Planarity :  0.005   0.043    601
  Dihedral  :  7.067  39.706    491
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.29 %
    Favored  : 85.71 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.98 (0.41), residues: 420
  helix: -2.06 (1.22), residues: 20
  sheet: -1.92 (0.39), residues: 142
  loop : -2.05 (0.41), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 466 
 TYR   0.020   0.002   TYR A 489 
 PHE   0.017   0.002   PHE L  98 
 TRP   0.041   0.003   TRP L  35 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 3411)
  covalent geometry    : angle       0.80530 ( 4635)
  SS BOND              : bond        0.00293 (    6)
  SS BOND              : angle       3.65208 (   12)
  hydrogen bonds       : bond        0.03602 (  100)
  hydrogen bonds       : angle       7.29683 (  228)
  link_NAG-ASN         : bond        0.01275 (    1)
  link_NAG-ASN         : angle       4.27055 (    3)

*********************** 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
  93 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: A  359 SER cc_start: 0.8502 (p) cc_final: 0.8296 (p)
REVERT: A  387 LEU cc_start: 0.7092 (tp) cc_final: 0.6890 (tp)
REVERT: A  417 LYS cc_start: 0.7906 (ptpt) cc_final: 0.7435 (tppt)
REVERT: A  439 ASN cc_start: 0.8196 (t0) cc_final: 0.7801 (t0)
REVERT: A  461 LEU cc_start: 0.6500 (mm) cc_final: 0.6043 (mm)
REVERT: A  462 LYS cc_start: 0.8474 (tppt) cc_final: 0.8045 (pttm)
REVERT: H   13 GLN cc_start: 0.6884 (mm-40) cc_final: 0.6412 (mm-40)
REVERT: H   29 PHE cc_start: 0.5883 (t80) cc_final: 0.5642 (t80)
REVERT: H  101 ARG cc_start: 0.7017 (tpt170) cc_final: 0.6311 (tmm160)
REVERT: H  122 VAL cc_start: 0.5489 (t) cc_final: 0.5253 (t)
REVERT: L   39 GLU cc_start: 0.7858 (pp20) cc_final: 0.6829 (tm-30)
REVERT: L   71 PHE cc_start: 0.7042 (m-10) cc_final: 0.6825 (m-10)
REVERT: L   92 PHE cc_start: 0.6226 (t80) cc_final: 0.5415 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.0600
  time to fit residues: 6.8373
Evaluate side-chains
  79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 9 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 20 optimal weight:    0.0570
   chunk 5 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 16 optimal weight:    0.2980
   overall best weight:    2.8704

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

Flipped N/Q/H residues before XYZ refinement:
H  39 GLN
L  34 ASN
L  38 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.163883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.139994 restraints weight = 5773.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.143583 restraints weight = 3665.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.145956 restraints weight = 2601.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.147671 restraints weight = 2022.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.149150 restraints weight = 1664.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6372
moved from start:          0.4897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3418  Z= 0.174
  Angle     :  0.840   7.917   4650  Z= 0.428
  Chirality :  0.049   0.172    501
  Planarity :  0.005   0.043    601
  Dihedral  :  7.143  39.072    491
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.29 %
    Favored  : 85.71 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.98 (0.41), residues: 420
  helix: -2.11 (1.18), residues: 20
  sheet: -1.89 (0.40), residues: 146
  loop : -2.05 (0.42), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 457 
 TYR   0.019   0.002   TYR L  49 
 PHE   0.019   0.002   PHE A 515 
 TRP   0.033   0.002   TRP L  35 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 3411)
  covalent geometry    : angle       0.81367 ( 4635)
  SS BOND              : bond        0.00246 (    6)
  SS BOND              : angle       3.60192 (   12)
  hydrogen bonds       : bond        0.03587 (  100)
  hydrogen bonds       : angle       7.35132 (  228)
  link_NAG-ASN         : bond        0.01231 (    1)
  link_NAG-ASN         : angle       4.29397 (    3)

*********************** 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
  88 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  359 SER cc_start: 0.8551 (p) cc_final: 0.8338 (p)
REVERT: A  417 LYS cc_start: 0.7880 (ptpt) cc_final: 0.7521 (tppt)
REVERT: A  439 ASN cc_start: 0.8197 (t0) cc_final: 0.7830 (t0)
REVERT: A  461 LEU cc_start: 0.6534 (mm) cc_final: 0.6045 (mm)
REVERT: A  462 LYS cc_start: 0.8438 (tppt) cc_final: 0.8028 (pttm)
REVERT: H   13 GLN cc_start: 0.6862 (mm-40) cc_final: 0.6361 (mm-40)
REVERT: H   29 PHE cc_start: 0.6043 (t80) cc_final: 0.5710 (t80)
REVERT: H  111 PHE cc_start: 0.8378 (m-10) cc_final: 0.8162 (m-10)
REVERT: H  122 VAL cc_start: 0.5503 (t) cc_final: 0.5299 (t)
REVERT: L   34 ASN cc_start: 0.7188 (m-40) cc_final: 0.6963 (m110)
REVERT: L   39 GLU cc_start: 0.7911 (pp20) cc_final: 0.6938 (tm-30)
REVERT: L   92 PHE cc_start: 0.6179 (t80) cc_final: 0.5342 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.0593
  time to fit residues: 6.4427
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  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 29 optimal weight:    0.1980
   chunk 24 optimal weight:    0.0470
   chunk 9 optimal weight:    0.8980
   chunk 33 optimal weight:    8.9990
   chunk 23 optimal weight:    6.9990
   chunk 32 optimal weight:   20.0000
   chunk 12 optimal weight:    5.9990
   chunk 31 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    1.2282

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.167247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.143588 restraints weight = 5810.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.147162 restraints weight = 3705.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.149741 restraints weight = 2637.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.151612 restraints weight = 2031.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.152761 restraints weight = 1651.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6265
moved from start:          0.4910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3418  Z= 0.127
  Angle     :  0.769   6.872   4650  Z= 0.390
  Chirality :  0.048   0.200    501
  Planarity :  0.005   0.040    601
  Dihedral  :  6.320  26.023    491
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.62 %
    Favored  : 87.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.90 (0.41), residues: 420
  helix: -2.35 (0.98), residues: 27
  sheet: -1.82 (0.41), residues: 146
  loop : -1.95 (0.42), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 101 
 TYR   0.018   0.002   TYR H  32 
 PHE   0.020   0.002   PHE A 497 
 TRP   0.019   0.002   TRP L  35 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 3411)
  covalent geometry    : angle       0.74412 ( 4635)
  SS BOND              : bond        0.00262 (    6)
  SS BOND              : angle       3.23535 (   12)
  hydrogen bonds       : bond        0.03256 (  100)
  hydrogen bonds       : angle       7.01424 (  228)
  link_NAG-ASN         : bond        0.01317 (    1)
  link_NAG-ASN         : angle       4.39697 (    3)

*********************** 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
  83 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
REVERT: A  387 LEU cc_start: 0.7156 (tp) cc_final: 0.6852 (tp)
REVERT: A  393 THR cc_start: 0.6455 (m) cc_final: 0.6177 (p)
REVERT: A  425 LEU cc_start: 0.8016 (mp) cc_final: 0.7772 (mp)
REVERT: A  439 ASN cc_start: 0.8140 (t0) cc_final: 0.7879 (t0)
REVERT: A  461 LEU cc_start: 0.6575 (mm) cc_final: 0.6243 (mm)
REVERT: A  462 LYS cc_start: 0.8365 (tppt) cc_final: 0.8015 (pttm)
REVERT: H   13 GLN cc_start: 0.6835 (mm-40) cc_final: 0.6379 (mm-40)
REVERT: H   29 PHE cc_start: 0.5882 (t80) cc_final: 0.5593 (t80)
REVERT: L   37 GLN cc_start: 0.5862 (pp30) cc_final: 0.5505 (pp30)
REVERT: L   39 GLU cc_start: 0.7943 (pp20) cc_final: 0.6842 (tm-30)
REVERT: L   92 PHE cc_start: 0.6314 (t80) cc_final: 0.5565 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0733
  time to fit residues: 7.3090
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  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 3 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 12 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0970
   chunk 35 optimal weight:    8.9990
   chunk 22 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
H  82 GLN
H  84 ASN
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.168632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.144663 restraints weight = 5842.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.148219 restraints weight = 3761.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.150764 restraints weight = 2709.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.152580 restraints weight = 2100.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.153765 restraints weight = 1729.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6265
moved from start:          0.5098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3418  Z= 0.130
  Angle     :  0.773   9.024   4650  Z= 0.390
  Chirality :  0.047   0.192    501
  Planarity :  0.005   0.037    601
  Dihedral  :  6.150  26.617    491
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.86 %
    Favored  : 87.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.73 (0.42), residues: 420
  helix: -2.17 (1.16), residues: 21
  sheet: -1.65 (0.41), residues: 145
  loop : -1.91 (0.42), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 457 
 TYR   0.018   0.002   TYR A 453 
 PHE   0.013   0.002   PHE L  71 
 TRP   0.018   0.002   TRP L  35 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 3411)
  covalent geometry    : angle       0.74802 ( 4635)
  SS BOND              : bond        0.00233 (    6)
  SS BOND              : angle       3.20706 (   12)
  hydrogen bonds       : bond        0.03302 (  100)
  hydrogen bonds       : angle       6.81177 (  228)
  link_NAG-ASN         : bond        0.01363 (    1)
  link_NAG-ASN         : angle       4.43221 (    3)

*********************** 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
  83 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
REVERT: A  387 LEU cc_start: 0.7199 (tp) cc_final: 0.6994 (tp)
REVERT: A  393 THR cc_start: 0.6449 (m) cc_final: 0.6180 (p)
REVERT: A  439 ASN cc_start: 0.8125 (t0) cc_final: 0.7871 (t0)
REVERT: A  461 LEU cc_start: 0.6598 (mm) cc_final: 0.6249 (mm)
REVERT: A  462 LYS cc_start: 0.8327 (tppt) cc_final: 0.7979 (pttm)
REVERT: H   13 GLN cc_start: 0.6850 (mm-40) cc_final: 0.6530 (pm20)
REVERT: H   29 PHE cc_start: 0.5990 (t80) cc_final: 0.5690 (t80)
REVERT: L   37 GLN cc_start: 0.5822 (pp30) cc_final: 0.5505 (pp30)
REVERT: L   39 GLU cc_start: 0.7947 (pp20) cc_final: 0.6882 (tm-30)
REVERT: L   92 PHE cc_start: 0.6383 (t80) cc_final: 0.5504 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0620
  time to fit residues: 6.3712
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  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 9 optimal weight:    8.9990
   chunk 6 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0970
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
L  34 ASN
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.167717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.144162 restraints weight = 5691.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.147623 restraints weight = 3705.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.150214 restraints weight = 2675.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.151831 restraints weight = 2076.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.153322 restraints weight = 1718.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6277
moved from start:          0.5240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   3418  Z= 0.144
  Angle     :  0.803   8.988   4650  Z= 0.407
  Chirality :  0.048   0.184    501
  Planarity :  0.005   0.040    601
  Dihedral  :  6.364  27.494    491
  Min Nonbonded Distance : 2.571

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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.78 (0.42), residues: 420
  helix: -2.38 (0.98), residues: 27
  sheet: -1.76 (0.41), residues: 146
  loop : -1.84 (0.42), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 457 
 TYR   0.012   0.002   TYR A 489 
 PHE   0.035   0.002   PHE H  68 
 TRP   0.025   0.002   TRP L  35 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 3411)
  covalent geometry    : angle       0.77251 ( 4635)
  SS BOND              : bond        0.00277 (    6)
  SS BOND              : angle       3.85240 (   12)
  hydrogen bonds       : bond        0.03408 (  100)
  hydrogen bonds       : angle       6.96345 (  228)
  link_NAG-ASN         : bond        0.01318 (    1)
  link_NAG-ASN         : angle       4.34747 (    3)

********************** 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
  82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.074 
Fit side-chains
   revert: symmetry clash
REVERT: A  393 THR cc_start: 0.6483 (m) cc_final: 0.6127 (p)
REVERT: A  439 ASN cc_start: 0.8179 (t0) cc_final: 0.7922 (t0)
REVERT: A  461 LEU cc_start: 0.6540 (mm) cc_final: 0.6168 (mm)
REVERT: A  462 LYS cc_start: 0.8323 (tppt) cc_final: 0.7977 (pttm)
REVERT: A  464 PHE cc_start: 0.6259 (m-10) cc_final: 0.5994 (m-10)
REVERT: H   13 GLN cc_start: 0.6903 (mm-40) cc_final: 0.6475 (pm20)
REVERT: H   29 PHE cc_start: 0.6021 (t80) cc_final: 0.5559 (t80)
REVERT: H  122 VAL cc_start: 0.5417 (t) cc_final: 0.5204 (t)
REVERT: L   37 GLN cc_start: 0.5934 (pp30) cc_final: 0.5562 (pp30)
REVERT: L   92 PHE cc_start: 0.6284 (t80) cc_final: 0.5525 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0617
  time to fit residues: 6.1843
Evaluate side-chains
  69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 29 optimal weight:    8.9990
   chunk 38 optimal weight:    8.9990
   chunk 37 optimal weight:   20.0000
   chunk 39 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:   10.0000
   chunk 28 optimal weight:    8.9990
   chunk 40 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    4.1988

-------------------------------------------------------------------------------
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 = 0.3894 r_free = 0.3894 target = 0.163049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.139826 restraints weight = 5972.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.143211 restraints weight = 3825.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.145633 restraints weight = 2754.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.147182 restraints weight = 2145.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.148402 restraints weight = 1781.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6419
moved from start:          0.5747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062   3418  Z= 0.238
  Angle     :  0.962  10.149   4650  Z= 0.492
  Chirality :  0.054   0.263    501
  Planarity :  0.007   0.069    601
  Dihedral  :  7.707  30.691    491
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 17.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.05 %
    Favored  : 85.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.22 (0.40), residues: 420
  helix: -2.56 (1.05), residues: 21
  sheet: -2.20 (0.40), residues: 144
  loop : -2.08 (0.40), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 355 
 TYR   0.022   0.003   TYR A 365 
 PHE   0.018   0.003   PHE L  71 
 TRP   0.047   0.004   TRP L  35 
 HIS   0.004   0.002   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 ( 3411)
  covalent geometry    : angle       0.92747 ( 4635)
  SS BOND              : bond        0.00304 (    6)
  SS BOND              : angle       4.74000 (   12)
  hydrogen bonds       : bond        0.04279 (  100)
  hydrogen bonds       : angle       7.60151 (  228)
  link_NAG-ASN         : bond        0.01321 (    1)
  link_NAG-ASN         : angle       3.82641 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 710.35 seconds
wall clock time: 12 minutes 55.01 seconds (775.01 seconds total)