Starting phenix.real_space_refine
on Fri Aug 22 17:34:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b7q_15899/08_2025/8b7q_15899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b7q_15899/08_2025/8b7q_15899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b7q_15899/08_2025/8b7q_15899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b7q_15899/08_2025/8b7q_15899.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b7q_15899/08_2025/8b7q_15899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b7q_15899/08_2025/8b7q_15899.map"
  }
  resolution = 4.02
  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=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3495 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    2236      2.51       5
     N     594      2.21       5
     O     663      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3511
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1064
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1064
          Classifications: {'peptide': 138}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 131}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1637
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1637
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 190}
    Chain: "F"
      Number of atoms: 796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 796
          Classifications: {'peptide': 97}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      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: 0.77, per 1000 atoms: 0.22
  Number of scatterers: 3511
  At special positions: 0
  Unit cell: (79.584, 98.651, 88.703, 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      18     16.00
     O     663      8.00
     N     594      7.00
     C    2236      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 117 " - pdb=" SG  CYS A 167 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 434 " - pdb=" SG  CYS B 445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 471 " - pdb=" SG  CYS B 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 486 " - pdb=" SG  CYS B 496 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 350 " - pdb=" SG  CYS F 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 411 " - pdb=" SG  CYS F 416 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG F 901 " - " ASN F 345 "
  Time building additional restraints: 0.18
  Conformation dependent library (CDL) restraints added in 95.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  850

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 8 sheets defined
      25.9% alpha, 32.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 45
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 3.870A  pdb=" N   GLN A  49 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   SER A  50 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 45 through 50'
    Processing helix  chain 'A' and resid 71 through 89
      removed outlier: 3.647A  pdb=" N   SER A  88 " --> pdb=" O   GLN A  84 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU A  89 " --> pdb=" O   VAL A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 113
    Processing helix  chain 'A' and resid 130 through 138
    Processing helix  chain 'A' and resid 138 through 162
      removed outlier: 4.117A  pdb=" N   ASP A 162 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 528 through 533
      removed outlier: 3.963A  pdb=" N   VAL B 533 " --> pdb=" O   ASP B 530 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 375 through 377
      No H-bonds generated for 'chain 'F' and resid 375 through 377'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 432 through 436
      removed outlier: 3.536A  pdb=" N   TRP B 447 " --> pdb=" O   TYR B 494 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 482 through 484
      removed outlier: 4.491A  pdb=" N   LEU B 462 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR B 459 " --> pdb=" O   ASN B 514 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 482 through 484
      removed outlier: 4.491A  pdb=" N   LEU B 462 " --> pdb=" O   LYS B 484 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR B 459 " --> pdb=" O   ASN B 514 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 539 through 546
      removed outlier: 5.035A  pdb=" N   ASN B 540 " --> pdb=" O   GLU B 557 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   GLU B 557 " --> pdb=" O   ASN B 540 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 582 through 586
    Processing sheet with id=AA6, first strand: chain 'F' and resid 331 through 334
    Processing sheet with id=AA7, first strand: chain 'F' and resid 331 through 334
      removed outlier: 3.552A  pdb=" N   ALA F 346 " --> pdb=" O   PHE F 391 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 337 through 340
      removed outlier: 7.582A  pdb=" N   HIS F 417 " --> pdb=" O   ASN F 412 " (cutoff:3.500A)
      removed outlier: 8.161A  pdb=" N   ASN F 412 " --> pdb=" O   HIS F 417 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ARG F 419 " --> pdb=" O   CYS F 410 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   CYS F 410 " --> pdb=" O   ARG F 419 " (cutoff:3.500A)

    175 hydrogen bonds defined for protein.
    474 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: 0.47

  Time building geometry restraints manager: 0.24 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1124
        1.34 -     1.46: 812
        1.46 -     1.58: 1630
        1.58 -     1.70: 0
        1.70 -     1.82: 22
  Bond restraints: 3588
  Sorted by residual:
  bond pdb=" C1  NAG F 901 "
       pdb=" O5  NAG F 901 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.75e+00
  bond pdb=" C5  NAG F 901 "
       pdb=" O5  NAG F 901 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.24e+00
  bond pdb=" C3  NAG F 901 "
       pdb=" O3  NAG F 901 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 9.76e-01
  bond pdb=" C   TRP B 447 "
       pdb=" N   SER B 448 "
    ideal  model  delta    sigma   weight residual
    1.332  1.347 -0.015 1.92e-02 2.71e+03 6.28e-01
  bond pdb=" N   SER A 114 "
       pdb=" CA  SER A 114 "
    ideal  model  delta    sigma   weight residual
    1.463  1.455  0.008 1.08e-02 8.57e+03 5.33e-01
  ... (remaining 3583 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 4692
        1.40 -     2.81: 165
        2.81 -     4.21: 26
        4.21 -     5.62: 1
        5.62 -     7.02: 1
  Bond angle restraints: 4885
  Sorted by residual:
  angle pdb=" C   ILE A  63 "
        pdb=" N   PRO A  64 "
        pdb=" CA  PRO A  64 "
      ideal   model   delta    sigma   weight residual
     119.84  122.92   -3.08 1.25e+00 6.40e-01 6.05e+00
  angle pdb=" C   PHE A 113 "
        pdb=" N   SER A 114 "
        pdb=" CA  SER A 114 "
      ideal   model   delta    sigma   weight residual
     120.89  124.35   -3.46 1.50e+00 4.44e-01 5.32e+00
  angle pdb=" N   SER A  46 "
        pdb=" CA  SER A  46 "
        pdb=" C   SER A  46 "
      ideal   model   delta    sigma   weight residual
     111.37  115.17   -3.80 1.65e+00 3.67e-01 5.30e+00
  angle pdb=" C   ILE A  45 "
        pdb=" N   SER A  46 "
        pdb=" CA  SER A  46 "
      ideal   model   delta    sigma   weight residual
     120.82  124.00   -3.18 1.50e+00 4.44e-01 4.50e+00
  angle pdb=" N   LEU B 503 "
        pdb=" CA  LEU B 503 "
        pdb=" C   LEU B 503 "
      ideal   model   delta    sigma   weight residual
     111.33  113.75   -2.42 1.21e+00 6.83e-01 4.01e+00
  ... (remaining 4880 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.92: 2086
       15.92 -    31.83: 94
       31.83 -    47.75: 22
       47.75 -    63.66: 4
       63.66 -    79.58: 2
  Dihedral angle restraints: 2208
    sinusoidal: 903
      harmonic: 1305
  Sorted by residual:
  dihedral pdb=" CB  CYS F 350 "
           pdb=" SG  CYS F 350 "
           pdb=" SG  CYS F 410 "
           pdb=" CB  CYS F 410 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   63.39   29.61     1      1.00e+01 1.00e-02 1.25e+01
  dihedral pdb=" N   LEU A 161 "
           pdb=" CA  LEU A 161 "
           pdb=" CB  LEU A 161 "
           pdb=" CG  LEU A 161 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.82  -58.18     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" N   PHE F 334 "
           pdb=" CA  PHE F 334 "
           pdb=" CB  PHE F 334 "
           pdb=" CG  PHE F 334 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -111.09   51.09     3      1.50e+01 4.44e-03 8.98e+00
  ... (remaining 2205 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 349
       0.031 -    0.062: 154
       0.062 -    0.092: 33
       0.092 -    0.123: 31
       0.123 -    0.154: 5
  Chirality restraints: 572
  Sorted by residual:
  chirality pdb=" CA  ILE F 351 "
            pdb=" N   ILE F 351 "
            pdb=" C   ILE F 351 "
            pdb=" CB  ILE F 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.91e-01
  chirality pdb=" CA  PRO A  64 "
            pdb=" N   PRO A  64 "
            pdb=" C   PRO A  64 "
            pdb=" CB  PRO A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.73e-01
  chirality pdb=" CA  ILE F 374 "
            pdb=" N   ILE F 374 "
            pdb=" C   ILE F 374 "
            pdb=" CB  ILE F 374 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  ... (remaining 569 not shown)

  Planarity restraints: 616
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 155 "    0.008 2.00e-02 2.50e+03   1.60e-02 2.57e+00
        pdb=" C   GLN A 155 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   GLN A 155 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASP A 156 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 448 "    0.023 5.00e-02 4.00e+02   3.52e-02 1.98e+00
        pdb=" N   PRO B 449 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B 449 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 449 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 148 "    0.006 2.00e-02 2.50e+03   1.28e-02 1.63e+00
        pdb=" C   SER A 148 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   SER A 148 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ARG A 149 "    0.007 2.00e-02 2.50e+03
  ... (remaining 613 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 532
        2.77 -     3.30: 3250
        3.30 -     3.83: 5553
        3.83 -     4.37: 6419
        4.37 -     4.90: 11088
  Nonbonded interactions: 26842
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 141 "
            pdb=" OH  TYR F 409 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   PRO A  64 "
            pdb=" OH  TYR A  82 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OD2 ASP A  30 "
            pdb=" OH  TYR B 470 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" NH2 ARG B 571 "
            pdb=" OE1 GLN B 608 "
     model   vdw
     2.362 3.120
  nonbonded pdb=" NH2 ARG F 400 "
            pdb=" O   TYR F 405 "
     model   vdw
     2.378 3.120
  ... (remaining 26837 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:             8.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.260
  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:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
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   0.026   3595  Z= 0.121
  Angle     :  0.601   7.021   4900  Z= 0.335
  Chirality :  0.043   0.154    572
  Planarity :  0.004   0.035    615
  Dihedral  :  9.873  79.577   1340
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  3.93 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  :  6.13 %
    Favored  : 90.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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 aren not related in a simple way.
  whole:  0.29 (0.38), residues: 433
  helix:  0.92 (0.47), residues: 97
  sheet:  0.83 (0.39), residues: 134
  loop : -0.57 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 467 
 TYR   0.009   0.001   TYR F 424 
 PHE   0.010   0.001   PHE B 493 
 TRP   0.006   0.001   TRP F 367 
 HIS   0.003   0.001   HIS B 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 3588)
  covalent geometry    : angle       0.59895 ( 4885)
  SS BOND              : bond        0.00220 (    6)
  SS BOND              : angle       0.89249 (   12)
  hydrogen bonds       : bond        0.18058 (  159)
  hydrogen bonds       : angle       7.45858 (  474)
  link_NAG-ASN         : bond        0.00028 (    1)
  link_NAG-ASN         : angle       1.67786 (    3)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.089 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ILE cc_start: 0.7042 (mt) cc_final: 0.6621 (mm)
REVERT: A   63 ILE cc_start: 0.8987 (mt) cc_final: 0.8664 (tt)
REVERT: A   93 ASN cc_start: 0.7569 (m-40) cc_final: 0.7287 (m-40)
REVERT: B  436 THR cc_start: 0.9047 (m) cc_final: 0.8331 (m)
REVERT: B  540 ASN cc_start: 0.8477 (t0) cc_final: 0.8226 (t0)
REVERT: B  565 ASN cc_start: 0.8276 (m-40) cc_final: 0.7795 (p0)
REVERT: B  572 TYR cc_start: 0.8019 (p90) cc_final: 0.7631 (p90)
REVERT: B  585 GLU cc_start: 0.8506 (mp0) cc_final: 0.8236 (pm20)
REVERT: B  609 VAL cc_start: 0.9427 (t) cc_final: 0.9200 (m)
REVERT: B  612 ARG cc_start: 0.8665 (ttt180) cc_final: 0.7832 (ttt-90)
REVERT: F  365 VAL cc_start: 0.8987 (m) cc_final: 0.8090 (p)
REVERT: F  388 LYS cc_start: 0.8796 (tttt) cc_final: 0.8555 (tttp)
REVERT: F  393 ASN cc_start: 0.7524 (t0) cc_final: 0.7077 (t0)
  outliers start: 12
  outliers final: 2
  residues processed: 155
  average time/residue: 0.0662
  time to fit residues: 12.3843
Evaluate side-chains
  97 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   chunk 30 optimal weight:    0.0010
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 369 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.112664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.092271 restraints weight = 8096.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.095016 restraints weight = 4744.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.096991 restraints weight = 3269.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.098331 restraints weight = 2505.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.099208 restraints weight = 2064.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.3412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3595  Z= 0.156
  Angle     :  0.669  10.878   4900  Z= 0.339
  Chirality :  0.046   0.261    572
  Planarity :  0.004   0.043    615
  Dihedral  :  4.372  17.048    496
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  1.72 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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 aren not related in a simple way.
  whole:  1.08 (0.40), residues: 433
  helix:  2.29 (0.50), residues: 103
  sheet:  0.52 (0.40), residues: 127
  loop :  0.12 (0.46), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 419 
 TYR   0.020   0.002   TYR A  82 
 PHE   0.011   0.002   PHE F 348 
 TRP   0.004   0.001   TRP B 620 
 HIS   0.004   0.001   HIS F 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 3588)
  covalent geometry    : angle       0.64098 ( 4885)
  SS BOND              : bond        0.01355 (    6)
  SS BOND              : angle       3.81696 (   12)
  hydrogen bonds       : bond        0.04131 (  159)
  hydrogen bonds       : angle       5.19639 (  474)
  link_NAG-ASN         : bond        0.00116 (    1)
  link_NAG-ASN         : angle       1.95340 (    3)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.8506 (ttpt) cc_final: 0.8119 (ttpt)
REVERT: A   93 ASN cc_start: 0.7657 (m-40) cc_final: 0.7431 (m-40)
REVERT: B  572 TYR cc_start: 0.8110 (p90) cc_final: 0.7719 (p90)
REVERT: B  609 VAL cc_start: 0.9493 (t) cc_final: 0.9282 (m)
REVERT: B  612 ARG cc_start: 0.8872 (ttt180) cc_final: 0.8353 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8655 (pt) cc_final: 0.8452 (mm)
REVERT: F  393 ASN cc_start: 0.7512 (t0) cc_final: 0.6967 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0578
  time to fit residues: 8.0310
Evaluate side-chains
  91 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0870
   chunk 8 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 41 optimal weight:    0.4980
   chunk 2 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 453 GLN
B 461 GLN
B 499 GLN
F 354 ASN
F 369 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.113822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.093016 restraints weight = 8074.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.095728 restraints weight = 4809.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.097619 restraints weight = 3352.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.098982 restraints weight = 2595.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.099839 restraints weight = 2154.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.4004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3595  Z= 0.122
  Angle     :  0.613  13.480   4900  Z= 0.312
  Chirality :  0.045   0.229    572
  Planarity :  0.004   0.032    615
  Dihedral  :  4.241  25.191    496
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  2.45 %
    Favored  : 97.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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 aren not related in a simple way.
  whole:  1.50 (0.41), residues: 433
  helix:  2.75 (0.50), residues: 102
  sheet:  0.57 (0.39), residues: 137
  loop :  0.48 (0.49), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 419 
 TYR   0.014   0.001   TYR F 352 
 PHE   0.011   0.001   PHE F 348 
 TRP   0.004   0.001   TRP B 447 
 HIS   0.002   0.001   HIS B 584 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 3588)
  covalent geometry    : angle       0.58889 ( 4885)
  SS BOND              : bond        0.01090 (    6)
  SS BOND              : angle       3.40831 (   12)
  hydrogen bonds       : bond        0.03709 (  159)
  hydrogen bonds       : angle       4.68286 (  474)
  link_NAG-ASN         : bond        0.00014 (    1)
  link_NAG-ASN         : angle       1.70414 (    3)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.145 
Fit side-chains
REVERT: B  429 ASN cc_start: 0.8904 (t0) cc_final: 0.8557 (t0)
REVERT: B  609 VAL cc_start: 0.9406 (t) cc_final: 0.9171 (m)
REVERT: B  612 ARG cc_start: 0.8859 (ttt180) cc_final: 0.8471 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8567 (pt) cc_final: 0.8272 (mm)
REVERT: F  393 ASN cc_start: 0.7455 (t0) cc_final: 0.6904 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0537
  time to fit residues: 7.4947
Evaluate side-chains
  85 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 22 optimal weight:    0.0970
   chunk 38 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 41 optimal weight:    0.4980
   chunk 6 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A  93 ASN
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 461 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.112534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.091930 restraints weight = 8033.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.094592 restraints weight = 4852.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.096438 restraints weight = 3419.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.097767 restraints weight = 2658.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.098604 restraints weight = 2206.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.4350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3595  Z= 0.138
  Angle     :  0.621  11.025   4900  Z= 0.313
  Chirality :  0.045   0.192    572
  Planarity :  0.004   0.033    615
  Dihedral  :  4.404  23.273    496
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  1.96 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    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 aren not related in a simple way.
  whole:  1.50 (0.41), residues: 433
  helix:  2.79 (0.51), residues: 102
  sheet:  0.83 (0.42), residues: 128
  loop :  0.25 (0.47), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 398 
 TYR   0.013   0.001   TYR F 352 
 PHE   0.009   0.001   PHE F 348 
 TRP   0.007   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 3588)
  covalent geometry    : angle       0.59808 ( 4885)
  SS BOND              : bond        0.00919 (    6)
  SS BOND              : angle       3.27803 (   12)
  hydrogen bonds       : bond        0.03790 (  159)
  hydrogen bonds       : angle       4.56825 (  474)
  link_NAG-ASN         : bond        0.00078 (    1)
  link_NAG-ASN         : angle       2.02971 (    3)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.087 
Fit side-chains
REVERT: B  429 ASN cc_start: 0.8902 (t0) cc_final: 0.8609 (t0)
REVERT: B  542 LYS cc_start: 0.8524 (mmmm) cc_final: 0.8272 (mmtm)
REVERT: B  572 TYR cc_start: 0.7982 (p90) cc_final: 0.7666 (p90)
REVERT: B  612 ARG cc_start: 0.8892 (ttt180) cc_final: 0.8548 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8617 (pt) cc_final: 0.8271 (mm)
REVERT: F  393 ASN cc_start: 0.7449 (t0) cc_final: 0.7090 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0562
  time to fit residues: 7.3530
Evaluate side-chains
  81 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 2 optimal weight:    0.1980
   chunk 1 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 461 GLN
F 369 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.111736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.090916 restraints weight = 8152.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.093532 restraints weight = 4941.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.095376 restraints weight = 3483.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.096697 restraints weight = 2710.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.097614 restraints weight = 2251.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.4580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3595  Z= 0.135
  Angle     :  0.632  12.121   4900  Z= 0.321
  Chirality :  0.045   0.200    572
  Planarity :  0.004   0.031    615
  Dihedral  :  4.480  31.960    496
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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 aren not related in a simple way.
  whole:  1.46 (0.41), residues: 433
  helix:  2.78 (0.51), residues: 102
  sheet:  0.85 (0.42), residues: 128
  loop :  0.17 (0.47), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 398 
 TYR   0.014   0.001   TYR A  82 
 PHE   0.008   0.001   PHE F 348 
 TRP   0.006   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 584 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 3588)
  covalent geometry    : angle       0.60576 ( 4885)
  SS BOND              : bond        0.00613 (    6)
  SS BOND              : angle       3.56157 (   12)
  hydrogen bonds       : bond        0.03728 (  159)
  hydrogen bonds       : angle       4.52048 (  474)
  link_NAG-ASN         : bond        0.00094 (    1)
  link_NAG-ASN         : angle       2.13156 (    3)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.086 
Fit side-chains
REVERT: B  429 ASN cc_start: 0.8876 (t0) cc_final: 0.8585 (t0)
REVERT: B  453 GLN cc_start: 0.8612 (pt0) cc_final: 0.8250 (pm20)
REVERT: B  542 LYS cc_start: 0.8562 (mmmm) cc_final: 0.8289 (mmtm)
REVERT: B  572 TYR cc_start: 0.7986 (p90) cc_final: 0.7599 (p90)
REVERT: B  612 ARG cc_start: 0.8863 (ttt180) cc_final: 0.8520 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8608 (pt) cc_final: 0.8352 (mm)
REVERT: F  393 ASN cc_start: 0.7406 (t0) cc_final: 0.6798 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0555
  time to fit residues: 6.6829
Evaluate side-chains
  80 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 7 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 369 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.109517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.088797 restraints weight = 8286.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.091367 restraints weight = 5125.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.093178 restraints weight = 3640.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.094414 restraints weight = 2838.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.095341 restraints weight = 2370.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.4831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3595  Z= 0.151
  Angle     :  0.637  10.424   4900  Z= 0.326
  Chirality :  0.046   0.188    572
  Planarity :  0.004   0.027    615
  Dihedral  :  4.669  33.191    496
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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 aren not related in a simple way.
  whole:  1.31 (0.41), residues: 433
  helix:  2.72 (0.51), residues: 102
  sheet:  0.78 (0.42), residues: 128
  loop :  0.01 (0.46), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 398 
 TYR   0.013   0.001   TYR F 424 
 PHE   0.010   0.001   PHE F 334 
 TRP   0.006   0.001   TRP B 447 
 HIS   0.004   0.001   HIS B 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 3588)
  covalent geometry    : angle       0.60972 ( 4885)
  SS BOND              : bond        0.00562 (    6)
  SS BOND              : angle       3.62845 (   12)
  hydrogen bonds       : bond        0.03832 (  159)
  hydrogen bonds       : angle       4.62574 (  474)
  link_NAG-ASN         : bond        0.00160 (    1)
  link_NAG-ASN         : angle       2.30239 (    3)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.084 
Fit side-chains
REVERT: B  429 ASN cc_start: 0.8831 (t0) cc_final: 0.8550 (t0)
REVERT: B  453 GLN cc_start: 0.8661 (pt0) cc_final: 0.8197 (pm20)
REVERT: B  542 LYS cc_start: 0.8598 (mmmm) cc_final: 0.8356 (mmtm)
REVERT: B  612 ARG cc_start: 0.8921 (ttt180) cc_final: 0.8504 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7463 (t0) cc_final: 0.6877 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.0472
  time to fit residues: 5.8698
Evaluate side-chains
  80 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 13 optimal weight:    0.0030
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 453 GLN
B 461 GLN
F 354 ASN
F 369 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.110634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.090020 restraints weight = 8035.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.092620 restraints weight = 4875.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.094428 restraints weight = 3416.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.095741 restraints weight = 2653.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.096676 restraints weight = 2195.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.4988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3595  Z= 0.129
  Angle     :  0.620   9.623   4900  Z= 0.316
  Chirality :  0.045   0.198    572
  Planarity :  0.004   0.026    615
  Dihedral  :  4.518  30.427    496
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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 aren not related in a simple way.
  whole:  1.29 (0.41), residues: 433
  helix:  2.57 (0.51), residues: 102
  sheet:  0.96 (0.42), residues: 127
  loop : -0.05 (0.46), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 613 
 TYR   0.009   0.001   TYR F 424 
 PHE   0.010   0.001   PHE F 334 
 TRP   0.005   0.001   TRP B 447 
 HIS   0.002   0.001   HIS B 584 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 3588)
  covalent geometry    : angle       0.59755 ( 4885)
  SS BOND              : bond        0.00487 (    6)
  SS BOND              : angle       3.20907 (   12)
  hydrogen bonds       : bond        0.03606 (  159)
  hydrogen bonds       : angle       4.57404 (  474)
  link_NAG-ASN         : bond        0.00063 (    1)
  link_NAG-ASN         : angle       2.08968 (    3)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.083 
Fit side-chains
REVERT: B  429 ASN cc_start: 0.8815 (t0) cc_final: 0.8544 (t0)
REVERT: B  453 GLN cc_start: 0.8614 (pt0) cc_final: 0.8148 (pm20)
REVERT: B  542 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8349 (mmtm)
REVERT: B  572 TYR cc_start: 0.7937 (p90) cc_final: 0.7623 (p90)
REVERT: B  610 ARG cc_start: 0.7153 (ptt180) cc_final: 0.6947 (ttp-170)
REVERT: B  612 ARG cc_start: 0.8880 (ttt180) cc_final: 0.8419 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7360 (t0) cc_final: 0.6645 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.0508
  time to fit residues: 6.3088
Evaluate side-chains
  79 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0970
   chunk 13 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 461 GLN
B 499 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.111154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.090407 restraints weight = 8214.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.092974 restraints weight = 5018.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.094791 restraints weight = 3557.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.096091 restraints weight = 2767.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.097017 restraints weight = 2303.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.5196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3595  Z= 0.144
  Angle     :  0.649   9.433   4900  Z= 0.331
  Chirality :  0.046   0.203    572
  Planarity :  0.004   0.028    615
  Dihedral  :  4.570  34.167    496
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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 aren not related in a simple way.
  whole:  1.25 (0.41), residues: 433
  helix:  2.32 (0.52), residues: 108
  sheet:  0.94 (0.42), residues: 127
  loop : -0.03 (0.46), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 385 
 TYR   0.011   0.001   TYR F 424 
 PHE   0.010   0.001   PHE F 334 
 TRP   0.007   0.001   TRP B 447 
 HIS   0.004   0.001   HIS B 584 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 3588)
  covalent geometry    : angle       0.62201 ( 4885)
  SS BOND              : bond        0.00407 (    6)
  SS BOND              : angle       3.65649 (   12)
  hydrogen bonds       : bond        0.03833 (  159)
  hydrogen bonds       : angle       4.69612 (  474)
  link_NAG-ASN         : bond        0.00121 (    1)
  link_NAG-ASN         : angle       2.21516 (    3)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.087 
Fit side-chains
REVERT: B  429 ASN cc_start: 0.8815 (t0) cc_final: 0.8391 (t0)
REVERT: B  542 LYS cc_start: 0.8547 (mmmm) cc_final: 0.8344 (mmtm)
REVERT: B  572 TYR cc_start: 0.7959 (p90) cc_final: 0.7635 (p90)
REVERT: B  612 ARG cc_start: 0.8887 (ttt180) cc_final: 0.8514 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7328 (t0) cc_final: 0.6574 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0580
  time to fit residues: 6.9668
Evaluate side-chains
  81 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 485 ASN
F 369 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.110209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.089651 restraints weight = 8086.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.092189 restraints weight = 4901.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.094048 restraints weight = 3458.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.095333 restraints weight = 2676.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.096160 restraints weight = 2216.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.5312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3595  Z= 0.167
  Angle     :  0.681   9.918   4900  Z= 0.350
  Chirality :  0.047   0.195    572
  Planarity :  0.004   0.031    615
  Dihedral  :  4.747  37.340    496
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  0.74 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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 aren not related in a simple way.
  whole:  1.15 (0.41), residues: 433
  helix:  2.42 (0.52), residues: 102
  sheet:  0.79 (0.43), residues: 128
  loop : -0.06 (0.46), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 385 
 TYR   0.012   0.001   TYR F 424 
 PHE   0.011   0.001   PHE F 334 
 TRP   0.008   0.001   TRP B 447 
 HIS   0.004   0.001   HIS B 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 3588)
  covalent geometry    : angle       0.65312 ( 4885)
  SS BOND              : bond        0.00456 (    6)
  SS BOND              : angle       3.78836 (   12)
  hydrogen bonds       : bond        0.03906 (  159)
  hydrogen bonds       : angle       4.88530 (  474)
  link_NAG-ASN         : bond        0.00200 (    1)
  link_NAG-ASN         : angle       2.42524 (    3)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.113 
Fit side-chains
REVERT: B  429 ASN cc_start: 0.8791 (t0) cc_final: 0.8376 (t0)
REVERT: B  453 GLN cc_start: 0.8712 (pt0) cc_final: 0.8168 (pm20)
REVERT: B  542 LYS cc_start: 0.8623 (mmmm) cc_final: 0.8387 (mmtm)
REVERT: B  572 TYR cc_start: 0.8004 (p90) cc_final: 0.7638 (p90)
REVERT: B  610 ARG cc_start: 0.7173 (ptt180) cc_final: 0.6958 (ttp-170)
REVERT: B  612 ARG cc_start: 0.8908 (ttt180) cc_final: 0.8574 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7372 (t0) cc_final: 0.6567 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0566
  time to fit residues: 7.0507
Evaluate side-chains
  81 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 29 optimal weight:    7.9990
   chunk 34 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 4 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 453 GLN
B 461 GLN
** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 369 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.110796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.089816 restraints weight = 8300.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.092344 restraints weight = 5129.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.094130 restraints weight = 3668.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.095400 restraints weight = 2877.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.096246 restraints weight = 2406.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.5468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3595  Z= 0.142
  Angle     :  0.646   9.263   4900  Z= 0.331
  Chirality :  0.046   0.220    572
  Planarity :  0.004   0.031    615
  Dihedral  :  4.658  37.067    496
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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 aren not related in a simple way.
  whole:  1.21 (0.41), residues: 433
  helix:  2.24 (0.51), residues: 108
  sheet:  0.93 (0.44), residues: 127
  loop : -0.03 (0.46), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 385 
 TYR   0.020   0.001   TYR A  82 
 PHE   0.011   0.001   PHE F 334 
 TRP   0.006   0.001   TRP B 447 
 HIS   0.005   0.001   HIS B 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 3588)
  covalent geometry    : angle       0.62020 ( 4885)
  SS BOND              : bond        0.00358 (    6)
  SS BOND              : angle       3.57430 (   12)
  hydrogen bonds       : bond        0.03867 (  159)
  hydrogen bonds       : angle       4.72514 (  474)
  link_NAG-ASN         : bond        0.00107 (    1)
  link_NAG-ASN         : angle       2.24237 (    3)

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

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

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  866 Ramachandran restraints generated.
    433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.118 
Fit side-chains
REVERT: B  429 ASN cc_start: 0.8780 (t0) cc_final: 0.8530 (t0)
REVERT: B  453 GLN cc_start: 0.8669 (pt0) cc_final: 0.8143 (pm20)
REVERT: B  612 ARG cc_start: 0.8910 (ttt180) cc_final: 0.8595 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7333 (t0) cc_final: 0.6471 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0597
  time to fit residues: 7.0951
Evaluate side-chains
  80 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 13 optimal weight:    0.4980
   chunk 8 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0570
   chunk 12 optimal weight:    0.5980
   chunk 31 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
B 465 HIS
F 369 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.111513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.090861 restraints weight = 8029.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.093356 restraints weight = 4911.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.095154 restraints weight = 3485.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.096458 restraints weight = 2721.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.097164 restraints weight = 2269.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.5542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3595  Z= 0.132
  Angle     :  0.663   8.878   4900  Z= 0.341
  Chirality :  0.046   0.178    572
  Planarity :  0.004   0.031    615
  Dihedral  :  4.636  36.440    496
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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 aren not related in a simple way.
  whole:  1.21 (0.41), residues: 433
  helix:  2.27 (0.52), residues: 109
  sheet:  0.81 (0.43), residues: 133
  loop :  0.01 (0.46), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 385 
 TYR   0.009   0.001   TYR F 424 
 PHE   0.009   0.001   PHE F 334 
 TRP   0.006   0.001   TRP B 447 
 HIS   0.006   0.001   HIS B 465 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 3588)
  covalent geometry    : angle       0.64025 ( 4885)
  SS BOND              : bond        0.00391 (    6)
  SS BOND              : angle       3.42120 (   12)
  hydrogen bonds       : bond        0.03645 (  159)
  hydrogen bonds       : angle       4.71430 (  474)
  link_NAG-ASN         : bond        0.00040 (    1)
  link_NAG-ASN         : angle       2.04633 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 868.50 seconds
wall clock time: 15 minutes 34.76 seconds (934.76 seconds total)