Starting phenix.real_space_refine
on Thu Jul  2 03:57:33 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8b7q_15899/07_2026/8b7q_15899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b7q_15899/07_2026/8b7q_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_15899/07_2026/8b7q_15899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b7q_15899/07_2026/8b7q_15899.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b7q_15899/07_2026/8b7q_15899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b7q_15899/07_2026/8b7q_15899.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8b7q_15899/07_2026/8b7q_15899.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8b7q_15899/07_2026/8b7q_15899.cif"
  }
  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-dev-6108/lib/python3.11/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 chiralities: 1
  Time building chain proxies: 0.98, per 1000 atoms: 0.28
  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: 0.29
  Conformation dependent library (CDL) restraints added in 124.5 milliseconds
  

  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: 0.11
  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: 0.50

  Time building geometry restraints manager: 0.39 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: 2067
       15.92 -    31.83: 94
       31.83 -    47.75: 20
       47.75 -    63.66: 4
       63.66 -    79.58: 2
  Dihedral angle restraints: 2187
    sinusoidal: 882
      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 2184 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:             8.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.200
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
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  :  9.836  79.577   1319
  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 are 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/Z
  covalent geometry    : bond        0.00265 /  0.12 ( 3588)
  covalent geometry    : angle       0.59895 /  0.33 ( 4885)
  SS BOND              : bond        0.00220 /  0.10 (    6)
  SS BOND              : angle       0.89249 /  0.55 (   12)
  hydrogen bonds       : bond        0.18058 / 12.48 (  159)
  hydrogen bonds       : angle       7.45858 /  5.04 (  474)
  link_NAG-ASN         : bond        0.00028 /  0.01 (    1)
  link_NAG-ASN         : angle       1.67786 /  0.81 (    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  : 0.130 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 ILE cc_start: 0.7042 (mt) cc_final: 0.6622 (mm)
REVERT: A   63 ILE cc_start: 0.8988 (mt) cc_final: 0.8665 (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: 0.8795 (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: 0.0723
  time to fit residues: 13.5208
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  : 0.132 
-------------------------------------------------------------------------------
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...
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 = 0.3602 r_free = 0.3602 target = 0.112728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.092257 restraints weight = 8091.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.095029 restraints weight = 4738.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.097003 restraints weight = 3265.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.098346 restraints weight = 2501.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.099248 restraints weight = 2061.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.3354

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     :  0.670  11.499   4900  Z= 0.338
  Chirality :  0.046   0.264    572
  Planarity :  0.004   0.044    615
  Dihedral  :  4.306  17.045    475
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  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 are not related in a simple way.
  whole:  1.12 (0.40), residues: 433
  helix:  2.28 (0.50), residues: 103
  sheet:  0.52 (0.38), residues: 136
  loop :  0.18 (0.48), residues: 194

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   0.012   0.002   PHE F 348 
 TRP   0.005   0.001   TRP B 620 
 HIS   0.004   0.001   HIS F 418 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.15 ( 3588)
  covalent geometry    : angle       0.64176 /  0.33 ( 4885)
  SS BOND              : bond        0.00749 /  0.29 (    6)
  SS BOND              : angle       3.82843 /  2.41 (   12)
  hydrogen bonds       : bond        0.04230 /  2.94 (  159)
  hydrogen bonds       : angle       5.22922 /  3.49 (  474)
  link_NAG-ASN         : bond        0.00083 /  0.04 (    1)
  link_NAG-ASN         : angle       1.74907 /  0.84 (    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
  115 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.8506 (ttpt) cc_final: 0.8126 (ttpt)
REVERT: A   93 ASN cc_start: 0.7603 (m-40) cc_final: 0.7389 (m-40)
REVERT: B  572 TYR cc_start: 0.8100 (p90) cc_final: 0.7717 (p90)
REVERT: B  609 VAL cc_start: 0.9490 (t) cc_final: 0.9277 (m)
REVERT: B  612 ARG cc_start: 0.8889 (ttt180) cc_final: 0.8370 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8679 (pt) cc_final: 0.8467 (mm)
REVERT: F  393 ASN cc_start: 0.7486 (t0) cc_final: 0.6928 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0628
  time to fit residues: 8.8865
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  : 0.134 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 35 optimal weight:    0.3980
   chunk 8 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  93 ASN
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3597 r_free = 0.3597 target = 0.112060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.091678 restraints weight = 8130.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.094229 restraints weight = 4943.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.096003 restraints weight = 3504.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.097310 restraints weight = 2748.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.097978 restraints weight = 2296.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.3960

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= 0.155
  Angle     :  0.642  13.981   4900  Z= 0.327
  Chirality :  0.046   0.236    572
  Planarity :  0.004   0.032    615
  Dihedral  :  4.464  25.338    475
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  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 are not related in a simple way.
  whole:  1.38 (0.41), residues: 433
  helix:  2.62 (0.50), residues: 102
  sheet:  0.70 (0.42), residues: 123
  loop :  0.27 (0.46), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 419 
 TYR   0.015   0.001   TYR F 352 
 PHE   0.011   0.001   PHE F 348 
 TRP   0.005   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.15 ( 3588)
  covalent geometry    : angle       0.61926 /  0.32 ( 4885)
  SS BOND              : bond        0.00800 /  0.36 (    6)
  SS BOND              : angle       3.35550 /  2.01 (   12)
  hydrogen bonds       : bond        0.03958 /  2.72 (  159)
  hydrogen bonds       : angle       4.83919 /  3.22 (  474)
  link_NAG-ASN         : bond        0.00093 /  0.05 (    1)
  link_NAG-ASN         : angle       2.04538 /  0.98 (    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
  105 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.136 
Fit side-chains
REVERT: B  429 ASN cc_start: 0.8908 (t0) cc_final: 0.8609 (t0)
REVERT: B  437 ASP cc_start: 0.8936 (p0) cc_final: 0.8720 (p0)
REVERT: B  609 VAL cc_start: 0.9431 (t) cc_final: 0.9184 (m)
REVERT: B  612 ARG cc_start: 0.8890 (ttt180) cc_final: 0.8500 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8628 (pt) cc_final: 0.8365 (mm)
REVERT: F  393 ASN cc_start: 0.7456 (t0) cc_final: 0.6899 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0623
  time to fit residues: 8.1589
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  : 0.139 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 41 optimal weight:    0.4980
   chunk 6 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 461 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.111927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.091286 restraints weight = 7995.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.093878 restraints weight = 4923.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.095659 restraints weight = 3511.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.096905 restraints weight = 2757.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.097736 restraints weight = 2313.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.4343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3595  Z= 0.136
  Angle     :  0.629  12.345   4900  Z= 0.317
  Chirality :  0.045   0.191    572
  Planarity :  0.004   0.030    615
  Dihedral  :  4.606  30.535    475
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.83
  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 are not related in a simple way.
  whole:  1.45 (0.41), residues: 433
  helix:  2.78 (0.51), residues: 102
  sheet:  0.84 (0.42), residues: 128
  loop :  0.16 (0.47), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 368 
 TYR   0.011   0.001   TYR F 424 
 PHE   0.009   0.001   PHE F 348 
 TRP   0.006   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.14 ( 3588)
  covalent geometry    : angle       0.60531 /  0.31 ( 4885)
  SS BOND              : bond        0.00636 /  0.28 (    6)
  SS BOND              : angle       3.32846 /  2.02 (   12)
  hydrogen bonds       : bond        0.03807 /  2.63 (  159)
  hydrogen bonds       : angle       4.62107 /  3.08 (  474)
  link_NAG-ASN         : bond        0.00070 /  0.04 (    1)
  link_NAG-ASN         : angle       2.13738 /  1.03 (    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
  103 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8441 (ttp80) cc_final: 0.8162 (ptm160)
REVERT: B  429 ASN cc_start: 0.8891 (t0) cc_final: 0.8603 (t0)
REVERT: B  572 TYR cc_start: 0.7993 (p90) cc_final: 0.7655 (p90)
REVERT: B  612 ARG cc_start: 0.8914 (ttt180) cc_final: 0.8545 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8633 (pt) cc_final: 0.8270 (mm)
REVERT: F  393 ASN cc_start: 0.7487 (t0) cc_final: 0.7064 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0671
  time to fit residues: 8.5230
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  : 0.137 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 35 optimal weight:    0.0770
   chunk 30 optimal weight:    0.2980
   chunk 2 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 6 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   chunk 36 optimal weight:    0.4980
   chunk 4 optimal weight:    0.2980
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.3338

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3614 r_free = 0.3614 target = 0.113415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.093094 restraints weight = 8150.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.095861 restraints weight = 4928.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.097759 restraints weight = 3432.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.099117 restraints weight = 2647.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.100026 restraints weight = 2183.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.4644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3595  Z= 0.107
  Angle     :  0.604  10.565   4900  Z= 0.306
  Chirality :  0.044   0.176    572
  Planarity :  0.004   0.029    615
  Dihedral  :  4.485  30.752    475
  Min Nonbonded Distance : 2.420

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 are not related in a simple way.
  whole:  1.50 (0.41), residues: 433
  helix:  2.95 (0.51), residues: 102
  sheet:  0.91 (0.42), residues: 127
  loop :  0.09 (0.47), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 398 
 TYR   0.008   0.001   TYR A  82 
 PHE   0.008   0.001   PHE F 348 
 TRP   0.006   0.001   TRP B 447 
 HIS   0.002   0.001   HIS B 584 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.11 ( 3588)
  covalent geometry    : angle       0.57972 /  0.30 ( 4885)
  SS BOND              : bond        0.00408 /  0.16 (    6)
  SS BOND              : angle       3.40836 /  2.06 (   12)
  hydrogen bonds       : bond        0.03568 /  2.47 (  159)
  hydrogen bonds       : angle       4.41667 /  2.95 (  474)
  link_NAG-ASN         : bond        0.00040 /  0.02 (    1)
  link_NAG-ASN         : angle       1.70684 /  0.83 (    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
  101 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8419 (ttp80) cc_final: 0.8146 (ptm160)
REVERT: B  429 ASN cc_start: 0.8888 (t0) cc_final: 0.8592 (t0)
REVERT: B  542 LYS cc_start: 0.8529 (mmmm) cc_final: 0.8273 (mmtm)
REVERT: B  572 TYR cc_start: 0.7982 (p90) cc_final: 0.7625 (p90)
REVERT: B  612 ARG cc_start: 0.8871 (ttt180) cc_final: 0.8537 (ttt-90)
REVERT: F  381 ILE cc_start: 0.8579 (pt) cc_final: 0.8306 (mm)
REVERT: F  393 ASN cc_start: 0.7341 (t0) cc_final: 0.6847 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0595
  time to fit residues: 7.5825
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  : 0.138 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 453 GLN
B 461 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.109188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.088964 restraints weight = 8274.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.091367 restraints weight = 5197.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.093055 restraints weight = 3749.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.094245 restraints weight = 2971.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.094983 restraints weight = 2504.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.4904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3595  Z= 0.225
  Angle     :  0.712  11.251   4900  Z= 0.363
  Chirality :  0.048   0.192    572
  Planarity :  0.004   0.038    615
  Dihedral  :  4.996  29.456    475
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  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 : 0.00 %

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:  1.10 (0.40), residues: 433
  helix:  2.34 (0.50), residues: 102
  sheet:  0.68 (0.39), residues: 139
  loop : -0.04 (0.47), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F 368 
 TYR   0.017   0.002   TYR F 424 
 PHE   0.013   0.002   PHE F 348 
 TRP   0.007   0.001   TRP F 366 
 HIS   0.006   0.001   HIS B 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00516 /  0.22 ( 3588)
  covalent geometry    : angle       0.68422 /  0.35 ( 4885)
  SS BOND              : bond        0.00896 /  0.39 (    6)
  SS BOND              : angle       3.75620 /  2.24 (   12)
  hydrogen bonds       : bond        0.04239 /  2.92 (  159)
  hydrogen bonds       : angle       5.00798 /  3.35 (  474)
  link_NAG-ASN         : bond        0.00343 /  0.18 (    1)
  link_NAG-ASN         : angle       2.94112 /  1.41 (    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
  101 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8166 (ptm160)
REVERT: B  429 ASN cc_start: 0.8849 (t0) cc_final: 0.8411 (t0)
REVERT: B  453 GLN cc_start: 0.8597 (pt0) cc_final: 0.8102 (pm20)
REVERT: B  542 LYS cc_start: 0.8558 (mmmm) cc_final: 0.8309 (mmtm)
REVERT: B  612 ARG cc_start: 0.8940 (ttt180) cc_final: 0.8589 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7504 (t0) cc_final: 0.6759 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0632
  time to fit residues: 8.0094
Evaluate side-chains
  78 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
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:    0.0870
   chunk 30 optimal weight:    0.0870
   chunk 27 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 41 optimal weight:    0.4980
   overall best weight:    0.4136

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 103 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 349 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 = 0.3590 r_free = 0.3590 target = 0.112006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.091526 restraints weight = 8111.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.094068 restraints weight = 4941.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.095867 restraints weight = 3500.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.097162 restraints weight = 2736.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.098017 restraints weight = 2284.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.5069

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= 0.120
  Angle     :  0.642   9.502   4900  Z= 0.329
  Chirality :  0.045   0.183    572
  Planarity :  0.004   0.028    615
  Dihedral  :  4.767  33.351    475
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  2.21 %
    Favored  : 97.55 %
  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 are not related in a simple way.
  whole:  1.18 (0.41), residues: 433
  helix:  2.31 (0.50), residues: 108
  sheet:  0.90 (0.42), residues: 127
  loop : -0.11 (0.46), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 398 
 TYR   0.009   0.001   TYR A  82 
 PHE   0.008   0.001   PHE F 334 
 TRP   0.005   0.001   TRP B 447 
 HIS   0.002   0.001   HIS B 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.12 ( 3588)
  covalent geometry    : angle       0.62020 /  0.32 ( 4885)
  SS BOND              : bond        0.00404 /  0.15 (    6)
  SS BOND              : angle       3.29830 /  2.01 (   12)
  hydrogen bonds       : bond        0.03624 /  2.50 (  159)
  hydrogen bonds       : angle       4.60454 /  3.12 (  474)
  link_NAG-ASN         : bond        0.00037 /  0.02 (    1)
  link_NAG-ASN         : angle       1.91083 /  0.93 (    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
  97 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8147 (ptm160)
REVERT: B  429 ASN cc_start: 0.8812 (t0) cc_final: 0.8557 (t0)
REVERT: B  542 LYS cc_start: 0.8530 (mmmm) cc_final: 0.8283 (mmtm)
REVERT: B  572 TYR cc_start: 0.7926 (p90) cc_final: 0.7622 (p90)
REVERT: B  612 ARG cc_start: 0.8867 (ttt180) cc_final: 0.8562 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7451 (t0) cc_final: 0.6827 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0626
  time to fit residues: 7.6068
Evaluate side-chains
  78 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 39 optimal weight:    0.3980
   chunk 41 optimal weight:    0.6980
   chunk 20 optimal weight:    0.1980
   chunk 6 optimal weight:    0.0030
   chunk 13 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
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 = 0.3599 r_free = 0.3599 target = 0.112109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.091825 restraints weight = 8166.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.094436 restraints weight = 4943.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.096256 restraints weight = 3457.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.097539 restraints weight = 2668.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.098488 restraints weight = 2204.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.5268

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= 0.118
  Angle     :  0.627   9.725   4900  Z= 0.319
  Chirality :  0.045   0.216    572
  Planarity :  0.004   0.030    615
  Dihedral  :  4.748  37.442    475
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  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 are not related in a simple way.
  whole:  1.25 (0.41), residues: 433
  helix:  2.42 (0.51), residues: 108
  sheet:  0.90 (0.44), residues: 127
  loop : -0.06 (0.46), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F 368 
 TYR   0.015   0.001   TYR A  82 
 PHE   0.007   0.001   PHE F 348 
 TRP   0.006   0.001   TRP B 447 
 HIS   0.002   0.001   HIS B 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 ( 3588)
  covalent geometry    : angle       0.59880 /  0.31 ( 4885)
  SS BOND              : bond        0.00381 /  0.14 (    6)
  SS BOND              : angle       3.70307 /  2.26 (   12)
  hydrogen bonds       : bond        0.03612 /  2.51 (  159)
  hydrogen bonds       : angle       4.55082 /  3.08 (  474)
  link_NAG-ASN         : bond        0.00021 /  0.01 (    1)
  link_NAG-ASN         : angle       1.65878 /  0.81 (    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
  95 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8402 (ttp80) cc_final: 0.8167 (ptm160)
REVERT: B  429 ASN cc_start: 0.8822 (t0) cc_final: 0.8590 (t0)
REVERT: B  542 LYS cc_start: 0.8554 (mmmm) cc_final: 0.8302 (mmtm)
REVERT: B  572 TYR cc_start: 0.7951 (p90) cc_final: 0.7672 (p90)
REVERT: B  612 ARG cc_start: 0.8878 (ttt180) cc_final: 0.8420 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7433 (t0) cc_final: 0.6574 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0616
  time to fit residues: 7.3087
Evaluate side-chains
  77 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 5 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0270
   chunk 15 optimal weight:    0.0470
   overall best weight:    0.4936

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 103 ASN
A 155 GLN
B 499 GLN
F 369 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.111987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.091829 restraints weight = 8103.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.094274 restraints weight = 5048.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.096008 restraints weight = 3622.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.097177 restraints weight = 2849.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.098066 restraints weight = 2406.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.5372

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= 0.124
  Angle     :  0.625   9.018   4900  Z= 0.319
  Chirality :  0.045   0.245    572
  Planarity :  0.004   0.030    615
  Dihedral  :  4.651  35.675    475
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  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 are not related in a simple way.
  whole:  1.22 (0.41), residues: 433
  helix:  2.27 (0.50), residues: 109
  sheet:  0.87 (0.43), residues: 133
  loop : -0.04 (0.47), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  41 
 TYR   0.013   0.001   TYR A  82 
 PHE   0.010   0.001   PHE F 334 
 TRP   0.007   0.001   TRP B 447 
 HIS   0.003   0.001   HIS B 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.12 ( 3588)
  covalent geometry    : angle       0.60080 /  0.31 ( 4885)
  SS BOND              : bond        0.00420 /  0.15 (    6)
  SS BOND              : angle       3.43105 /  2.09 (   12)
  hydrogen bonds       : bond        0.03596 /  2.45 (  159)
  hydrogen bonds       : angle       4.55260 /  3.08 (  474)
  link_NAG-ASN         : bond        0.00022 /  0.01 (    1)
  link_NAG-ASN         : angle       1.78511 /  0.87 (    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
  102 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 ARG cc_start: 0.8405 (ttp80) cc_final: 0.8177 (ptm160)
REVERT: B  429 ASN cc_start: 0.8809 (t0) cc_final: 0.8583 (t0)
REVERT: B  542 LYS cc_start: 0.8514 (mmmm) cc_final: 0.8305 (mmtm)
REVERT: B  610 ARG cc_start: 0.7117 (ptt180) cc_final: 0.6822 (ttp-170)
REVERT: B  612 ARG cc_start: 0.8900 (ttt180) cc_final: 0.8457 (ttt-90)
REVERT: F  393 ASN cc_start: 0.7448 (t0) cc_final: 0.6589 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0720
  time to fit residues: 9.0735
Evaluate side-chains
  82 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 29 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 103 ASN
B 461 GLN
B 499 GLN
F 369 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.109507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.089244 restraints weight = 8339.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.091677 restraints weight = 5248.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.093372 restraints weight = 3774.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.094357 restraints weight = 2970.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.095417 restraints weight = 2531.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.5530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3595  Z= 0.164
  Angle     :  0.657   9.121   4900  Z= 0.336
  Chirality :  0.046   0.223    572
  Planarity :  0.004   0.033    615
  Dihedral  :  4.837  34.393    475
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  0.49 %
    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 are not related in a simple way.
  whole:  1.12 (0.41), residues: 433
  helix:  2.43 (0.51), residues: 103
  sheet:  0.90 (0.45), residues: 129
  loop : -0.22 (0.45), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 149 
 TYR   0.013   0.001   TYR F 424 
 PHE   0.013   0.002   PHE F 334 
 TRP   0.006   0.001   TRP B 447 
 HIS   0.004   0.001   HIS B 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.16 ( 3588)
  covalent geometry    : angle       0.63219 /  0.33 ( 4885)
  SS BOND              : bond        0.00429 /  0.15 (    6)
  SS BOND              : angle       3.51241 /  2.12 (   12)
  hydrogen bonds       : bond        0.03735 /  2.58 (  159)
  hydrogen bonds       : angle       4.72579 /  3.20 (  474)
  link_NAG-ASN         : bond        0.00178 /  0.09 (    1)
  link_NAG-ASN         : angle       2.31021 /  1.11 (    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
  98 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A   56 ARG cc_start: 0.8415 (ttp80) cc_final: 0.8168 (ptm160)
REVERT: A   75 MET cc_start: 0.7279 (ptp) cc_final: 0.6962 (ptp)
REVERT: B  429 ASN cc_start: 0.8796 (t0) cc_final: 0.8422 (t0)
REVERT: B  542 LYS cc_start: 0.8517 (mmmm) cc_final: 0.8313 (mmtm)
REVERT: B  610 ARG cc_start: 0.7131 (ptt180) cc_final: 0.6931 (ttp-170)
REVERT: F  393 ASN cc_start: 0.7386 (t0) cc_final: 0.6515 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0638
  time to fit residues: 7.7617
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  : 0.135 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 31 optimal weight:    6.9990
   chunk 38 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 103 ASN
B 461 GLN
B 499 GLN
F 369 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.109831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.089857 restraints weight = 8118.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.092268 restraints weight = 5156.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.093952 restraints weight = 3715.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.095134 restraints weight = 2937.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.095935 restraints weight = 2474.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.5593

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= 0.148
  Angle     :  0.649   8.821   4900  Z= 0.334
  Chirality :  0.046   0.267    572
  Planarity :  0.004   0.030    615
  Dihedral  :  4.758  33.336    475
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  0.98 %
    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 are not related in a simple way.
  whole:  1.08 (0.41), residues: 433
  helix:  2.10 (0.50), residues: 109
  sheet:  0.69 (0.43), residues: 138
  loop : -0.03 (0.48), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 612 
 TYR   0.015   0.001   TYR A  82 
 PHE   0.011   0.001   PHE F 334 
 TRP   0.008   0.001   TRP B 620 
 HIS   0.004   0.001   HIS B 465 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.15 ( 3588)
  covalent geometry    : angle       0.62506 /  0.32 ( 4885)
  SS BOND              : bond        0.00376 /  0.14 (    6)
  SS BOND              : angle       3.38679 /  2.06 (   12)
  hydrogen bonds       : bond        0.03767 /  2.57 (  159)
  hydrogen bonds       : angle       4.64215 /  3.13 (  474)
  link_NAG-ASN         : bond        0.00146 /  0.08 (    1)
  link_NAG-ASN         : angle       2.20612 /  1.07 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1016.48 seconds
wall clock time: 18 minutes 16.46 seconds (1096.46 seconds total)