Starting phenix.real_space_refine
on Tue Mar  3 11:23:23 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e39_30977/03_2026/7e39_30977.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e39_30977/03_2026/7e39_30977.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e39_30977/03_2026/7e39_30977.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e39_30977/03_2026/7e39_30977.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e39_30977/03_2026/7e39_30977.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e39_30977/03_2026/7e39_30977.map"
  }
  resolution = 3.7
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    1946      2.51       5
     N     525      2.21       5
     O     588      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3074
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
    Chain: "B"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 6, 'TRANS': 99}
    Chain: "C"
      Number of atoms: 705
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 705
          Classifications: {'peptide': 114}
          Incomplete info: {'truncation_to_alanine': 58}
          Link IDs: {'PTRANS': 2, 'TRANS': 111}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 187
          Unresolved non-hydrogen angles: 238
          Unresolved non-hydrogen dihedrals: 152
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ARG:plan': 4, 'PHE:plan': 3, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 97
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 0.84, per 1000 atoms: 0.27
  Number of scatterers: 3074
  At special positions: 0
  Unit cell: (56.16, 103.68, 76.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      15     16.00
     O     588      8.00
     N     525      7.00
     C    1946      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " 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 A 601 " - " ASN A 343 "
  Time building additional restraints: 0.21
  Conformation dependent library (CDL) restraints added in 101.8 milliseconds
  

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  756

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 8 sheets defined
      11.4% alpha, 29.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 367 through 372
      removed outlier: 3.799A  pdb=" N   ALA A 372 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 4.173A  pdb=" N   ASN A 388 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.665A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'B' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 4.037A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLU A 516 " --> pdb=" O   ASN A 394 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   TYR A 396 " --> pdb=" O   SER A 514 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   SER A 514 " --> pdb=" O   TYR A 396 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
      removed outlier: 3.613A  pdb=" N   TYR A 489 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 6
      removed outlier: 6.210A  pdb=" N   THR B  69 " --> pdb=" O   ALA B  25 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12
      removed outlier: 5.769A  pdb=" N   MET B  11 " --> pdb=" O   LEU B 104 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54
      removed outlier: 3.527A  pdb=" N   TYR B  49 " --> pdb=" O   SER B  53 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   TYR B  49 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   LEU B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.713A  pdb=" N   VAL C 114 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 6.067A  pdb=" N   ARG C  38 " --> pdb=" O   TRP C  47 " (cutoff:3.500A)
      removed outlier: 5.146A  pdb=" N   TRP C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)

    94 hydrogen bonds defined for protein.
    225 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: 0.44

  Time building geometry restraints manager: 0.31 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1003
        1.34 -     1.46: 799
        1.46 -     1.58: 1330
        1.58 -     1.70: 0
        1.70 -     1.82: 18
  Bond restraints: 3150
  Sorted by residual:
  bond pdb=" CG  LEU A 387 "
       pdb=" CD1 LEU A 387 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.45e+00
  bond pdb=" C5  NAG A 601 "
       pdb=" O5  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.26e+00
  bond pdb=" C3  NAG A 601 "
       pdb=" O3  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.403  1.424 -0.021 2.00e-02 2.50e+03 1.07e+00
  bond pdb=" CB  CYS A 480 "
       pdb=" SG  CYS A 480 "
    ideal  model  delta    sigma   weight residual
    1.808  1.774  0.034 3.30e-02 9.18e+02 1.06e+00
  bond pdb=" CG  LEU A 455 "
       pdb=" CD2 LEU A 455 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.26e-01
  ... (remaining 3145 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 4093
        1.62 -     3.24: 164
        3.24 -     4.86: 29
        4.86 -     6.48: 3
        6.48 -     8.10: 3
  Bond angle restraints: 4292
  Sorted by residual:
  angle pdb=" N   GLY C 111 "
        pdb=" CA  GLY C 111 "
        pdb=" C   GLY C 111 "
      ideal   model   delta    sigma   weight residual
     113.18  118.81   -5.63 2.37e+00 1.78e-01 5.65e+00
  angle pdb=" CA  TYR B  94 "
        pdb=" CB  TYR B  94 "
        pdb=" CG  TYR B  94 "
      ideal   model   delta    sigma   weight residual
     113.90  109.63    4.27 1.80e+00 3.09e-01 5.62e+00
  angle pdb=" C   GLN B  79 "
        pdb=" CA  GLN B  79 "
        pdb=" CB  GLN B  79 "
      ideal   model   delta    sigma   weight residual
     109.26  112.71   -3.45 1.47e+00 4.63e-01 5.51e+00
  angle pdb=" C   GLY B  66 "
        pdb=" N   SER B  67 "
        pdb=" CA  SER B  67 "
      ideal   model   delta    sigma   weight residual
     121.87  117.62    4.25 1.83e+00 2.99e-01 5.38e+00
  angle pdb=" CA  LEU A 455 "
        pdb=" CB  LEU A 455 "
        pdb=" CG  LEU A 455 "
      ideal   model   delta    sigma   weight residual
     116.30  124.40   -8.10 3.50e+00 8.16e-02 5.36e+00
  ... (remaining 4287 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.32: 1588
       14.32 -    28.63: 184
       28.63 -    42.95: 52
       42.95 -    57.26: 12
       57.26 -    71.58: 7
  Dihedral angle restraints: 1843
    sinusoidal: 652
      harmonic: 1191
  Sorted by residual:
  dihedral pdb=" CA  LEU B  78 "
           pdb=" C   LEU B  78 "
           pdb=" N   GLN B  79 "
           pdb=" CA  GLN B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.27   25.73     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  SER B  67 "
           pdb=" C   SER B  67 "
           pdb=" N   GLU B  68 "
           pdb=" CA  GLU B  68 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.90   24.10     0      5.00e+00 4.00e-02 2.32e+01
  dihedral pdb=" CA  GLN B  79 "
           pdb=" C   GLN B  79 "
           pdb=" N   PRO B  80 "
           pdb=" CA  PRO B  80 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.55  -23.45     0      5.00e+00 4.00e-02 2.20e+01
  ... (remaining 1840 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 310
       0.041 -    0.083: 104
       0.083 -    0.124: 40
       0.124 -    0.166: 11
       0.166 -    0.207: 1
  Chirality restraints: 466
  Sorted by residual:
  chirality pdb=" C1  NAG A 601 "
            pdb=" ND2 ASN A 343 "
            pdb=" C2  NAG A 601 "
            pdb=" O5  NAG A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.19   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  ILE A 358 "
            pdb=" N   ILE A 358 "
            pdb=" C   ILE A 358 "
            pdb=" CB  ILE A 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.35e-01
  chirality pdb=" CA  VAL B  43 "
            pdb=" N   VAL B  43 "
            pdb=" C   VAL B  43 "
            pdb=" CB  VAL B  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.30e-01
  ... (remaining 463 not shown)

  Planarity restraints: 563
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B  94 "   -0.038 5.00e-02 4.00e+02   5.74e-02 5.27e+00
        pdb=" N   PRO B  95 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO B  95 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B  95 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B  79 "   -0.032 5.00e-02 4.00e+02   4.95e-02 3.93e+00
        pdb=" N   PRO B  80 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO B  80 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B  80 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 456 "    0.004 2.00e-02 2.50e+03   1.34e-02 3.14e+00
        pdb=" CG  PHE A 456 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 456 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 456 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 456 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 456 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 456 "    0.001 2.00e-02 2.50e+03
  ... (remaining 560 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 93
        2.68 -     3.24: 3074
        3.24 -     3.79: 4685
        3.79 -     4.35: 6276
        4.35 -     4.90: 10301
  Nonbonded interactions: 24429
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B  39 "
            pdb=" O   GLU B  81 "
     model   vdw
     2.130 3.120
  nonbonded pdb=" OG  SER B  63 "
            pdb=" OG1 THR B  74 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" NZ  LYS B  39 "
            pdb=" OE2 GLU B  81 "
     model   vdw
     2.172 3.120
  nonbonded pdb=" NH2 ARG A 454 "
            pdb=" O   SER A 469 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" O   TYR B  49 "
            pdb=" OG  SER B  53 "
     model   vdw
     2.225 3.040
  ... (remaining 24424 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:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.760
  Find NCS groups from input model:        0.030
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
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      :  0.005   0.040   3156  Z= 0.215
  Angle     :  0.776   8.104   4305  Z= 0.421
  Chirality :  0.050   0.207    466
  Planarity :  0.005   0.057    562
  Dihedral  : 14.331  71.576   1072
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 15.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.52 (0.38), residues: 406
  helix: -3.93 (0.60), residues: 33
  sheet: -1.59 (0.43), residues: 131
  loop : -2.63 (0.36), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 457 
 TYR   0.023   0.002   TYR B  94 
 PHE   0.024   0.002   PHE A 456 
 TRP   0.012   0.002   TRP C  52 
 HIS   0.005   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 3150)
  covalent geometry    : angle       0.76795 ( 4292)
  SS BOND              : bond        0.00328 (    5)
  SS BOND              : angle       2.15827 (   10)
  hydrogen bonds       : bond        0.18706 (   94)
  hydrogen bonds       : angle       9.64269 (  225)
  link_NAG-ASN         : bond        0.00010 (    1)
  link_NAG-ASN         : angle       2.14049 (    3)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.104 
Fit side-chains
REVERT: A  389 ASP cc_start: 0.7162 (t0) cc_final: 0.6787 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0726
  time to fit residues: 3.4767
Evaluate side-chains
  34 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.0980
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:    8.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:   20.0000
   chunk 25 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0870
   chunk 22 optimal weight:    4.9990
   chunk 37 optimal weight:    9.9990
   overall best weight:    3.4364

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

Flipped N/Q/H residues before XYZ refinement:
A 501 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.068757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.061493 restraints weight = 14615.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.062864 restraints weight = 8026.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.063729 restraints weight = 5236.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.064329 restraints weight = 3902.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.064719 restraints weight = 3119.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.0984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3156  Z= 0.224
  Angle     :  0.719   6.473   4305  Z= 0.377
  Chirality :  0.050   0.169    466
  Planarity :  0.006   0.057    562
  Dihedral  :  6.316  24.526    471
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.07 %
    Favored  : 87.93 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  9.18 %
    Favored  : 89.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.35 (0.38), residues: 406
  helix: -3.92 (0.83), residues: 20
  sheet: -1.61 (0.42), residues: 134
  loop : -2.53 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  98 
 TYR   0.022   0.002   TYR B  94 
 PHE   0.022   0.002   PHE A 456 
 TRP   0.012   0.002   TRP C  52 
 HIS   0.006   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 3150)
  covalent geometry    : angle       0.71309 ( 4292)
  SS BOND              : bond        0.00357 (    5)
  SS BOND              : angle       1.77799 (   10)
  hydrogen bonds       : bond        0.04101 (   94)
  hydrogen bonds       : angle       7.78407 (  225)
  link_NAG-ASN         : bond        0.00121 (    1)
  link_NAG-ASN         : angle       1.83734 (    3)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A  365 TYR cc_start: 0.7430 (m-80) cc_final: 0.6694 (m-80)
REVERT: A  389 ASP cc_start: 0.7096 (t0) cc_final: 0.6716 (t0)
  outliers start: 4
  outliers final: 2
  residues processed: 36
  average time/residue: 0.0766
  time to fit residues: 3.3840
Evaluate side-chains
  34 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue   21 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:   20.0000
   chunk 1 optimal weight:    3.9990
   chunk 20 optimal weight:   20.0000
   chunk 8 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 25 optimal weight:   20.0000
   chunk 37 optimal weight:   20.0000
   chunk 14 optimal weight:    0.8980
   chunk 3 optimal weight:    0.4980
   chunk 13 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.070222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.063043 restraints weight = 14195.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.064453 restraints weight = 7528.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.065364 restraints weight = 4840.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.065972 restraints weight = 3524.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.066380 restraints weight = 2796.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.1398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3156  Z= 0.129
  Angle     :  0.614   8.661   4305  Z= 0.318
  Chirality :  0.048   0.189    466
  Planarity :  0.005   0.063    562
  Dihedral  :  5.496  23.733    471
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.39 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 12.93 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.08 (0.39), residues: 406
  helix: -3.25 (0.91), residues: 21
  sheet: -1.41 (0.43), residues: 137
  loop : -2.40 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  98 
 TYR   0.017   0.001   TYR B  94 
 PHE   0.023   0.001   PHE A 456 
 TRP   0.008   0.001   TRP C  52 
 HIS   0.004   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 3150)
  covalent geometry    : angle       0.61091 ( 4292)
  SS BOND              : bond        0.00140 (    5)
  SS BOND              : angle       1.06500 (   10)
  hydrogen bonds       : bond        0.03045 (   94)
  hydrogen bonds       : angle       7.03530 (  225)
  link_NAG-ASN         : bond        0.00040 (    1)
  link_NAG-ASN         : angle       1.71621 (    3)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A  365 TYR cc_start: 0.7443 (m-80) cc_final: 0.6857 (m-80)
  outliers start: 6
  outliers final: 6
  residues processed: 40
  average time/residue: 0.0669
  time to fit residues: 3.3425
Evaluate side-chains
  41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue  100 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 31 optimal weight:   20.0000
   chunk 37 optimal weight:   20.0000
   chunk 13 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 6 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.068760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.061601 restraints weight = 14491.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.062962 restraints weight = 7859.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.063870 restraints weight = 5094.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.064401 restraints weight = 3734.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.064818 restraints weight = 3029.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3156  Z= 0.236
  Angle     :  0.692   7.618   4305  Z= 0.362
  Chirality :  0.049   0.174    466
  Planarity :  0.006   0.063    562
  Dihedral  :  6.098  25.906    471
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.05 %
    Favored  : 86.95 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 15.31 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.13 (0.39), residues: 406
  helix: -3.13 (1.01), residues: 21
  sheet: -1.52 (0.41), residues: 143
  loop : -2.40 (0.38), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  18 
 TYR   0.027   0.002   TYR B  94 
 PHE   0.014   0.002   PHE A 377 
 TRP   0.011   0.002   TRP A 353 
 HIS   0.005   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 ( 3150)
  covalent geometry    : angle       0.68718 ( 4292)
  SS BOND              : bond        0.00370 (    5)
  SS BOND              : angle       1.54585 (   10)
  hydrogen bonds       : bond        0.03668 (   94)
  hydrogen bonds       : angle       7.29823 (  225)
  link_NAG-ASN         : bond        0.00007 (    1)
  link_NAG-ASN         : angle       1.90915 (    3)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A  365 TYR cc_start: 0.7500 (m-80) cc_final: 0.6800 (m-80)
  outliers start: 10
  outliers final: 7
  residues processed: 37
  average time/residue: 0.0624
  time to fit residues: 2.9140
Evaluate side-chains
  39 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain A residue  489 TYR
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue  100 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    9.9990
   chunk 17 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.9784

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.070471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.063376 restraints weight = 14334.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.064779 restraints weight = 7499.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.065654 restraints weight = 4761.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.066269 restraints weight = 3485.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.066530 restraints weight = 2744.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3156  Z= 0.110
  Angle     :  0.596   7.874   4305  Z= 0.307
  Chirality :  0.047   0.206    466
  Planarity :  0.005   0.065    562
  Dihedral  :  5.185  23.368    471
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 18.03 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.85 (0.40), residues: 406
  helix: -2.85 (1.05), residues: 21
  sheet: -1.44 (0.41), residues: 150
  loop : -2.15 (0.39), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  98 
 TYR   0.012   0.001   TYR B  94 
 PHE   0.013   0.001   PHE A 456 
 TRP   0.008   0.001   TRP C  52 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 3150)
  covalent geometry    : angle       0.59309 ( 4292)
  SS BOND              : bond        0.00097 (    5)
  SS BOND              : angle       0.87506 (   10)
  hydrogen bonds       : bond        0.02885 (   94)
  hydrogen bonds       : angle       6.60160 (  225)
  link_NAG-ASN         : bond        0.00061 (    1)
  link_NAG-ASN         : angle       2.02584 (    3)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 38
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A  365 TYR cc_start: 0.7482 (m-80) cc_final: 0.6721 (m-80)
  outliers start: 10
  outliers final: 6
  residues processed: 44
  average time/residue: 0.0755
  time to fit residues: 4.0355
Evaluate side-chains
  41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain A residue  489 TYR
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain C residue  100 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   chunk 14 optimal weight:    8.9990
   chunk 35 optimal weight:   30.0000
   chunk 5 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 20 optimal weight:   10.0000
   chunk 19 optimal weight:    0.1980
   chunk 31 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   overall best weight:    3.0186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.069062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.062024 restraints weight = 14289.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.063367 restraints weight = 7743.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.064256 restraints weight = 5021.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.064851 restraints weight = 3678.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.065175 restraints weight = 2925.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3156  Z= 0.196
  Angle     :  0.654   8.327   4305  Z= 0.339
  Chirality :  0.048   0.176    466
  Planarity :  0.005   0.063    562
  Dihedral  :  5.626  23.553    471
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.08 %
    Favored  : 88.92 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 19.05 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.90 (0.40), residues: 406
  helix: -2.98 (1.02), residues: 21
  sheet: -1.34 (0.42), residues: 143
  loop : -2.27 (0.38), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  26 
 TYR   0.020   0.002   TYR B  94 
 PHE   0.012   0.002   PHE A 456 
 TRP   0.009   0.002   TRP C  52 
 HIS   0.004   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 3150)
  covalent geometry    : angle       0.65028 ( 4292)
  SS BOND              : bond        0.00286 (    5)
  SS BOND              : angle       1.29279 (   10)
  hydrogen bonds       : bond        0.03293 (   94)
  hydrogen bonds       : angle       6.79992 (  225)
  link_NAG-ASN         : bond        0.00090 (    1)
  link_NAG-ASN         : angle       1.69608 (    3)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 33
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A  365 TYR cc_start: 0.7514 (m-80) cc_final: 0.6947 (m-80)
REVERT: A  493 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6765 (tm-30)
  outliers start: 11
  outliers final: 9
  residues processed: 38
  average time/residue: 0.0632
  time to fit residues: 3.0144
Evaluate side-chains
  43 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 33
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain A residue  489 TYR
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  101 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0670
   chunk 13 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 36 optimal weight:   30.0000
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 38 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.8126

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.069812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.062615 restraints weight = 14408.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.064034 restraints weight = 7635.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.064981 restraints weight = 4860.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.065603 restraints weight = 3507.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.065984 restraints weight = 2754.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3156  Z= 0.139
  Angle     :  0.610   8.555   4305  Z= 0.314
  Chirality :  0.047   0.194    466
  Planarity :  0.005   0.065    562
  Dihedral  :  5.302  22.498    471
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 18.71 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.90 (0.40), residues: 406
  helix: -2.95 (1.00), residues: 21
  sheet: -1.59 (0.39), residues: 162
  loop : -2.07 (0.41), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  98 
 TYR   0.017   0.001   TYR B  94 
 PHE   0.011   0.001   PHE A 456 
 TRP   0.009   0.001   TRP C  52 
 HIS   0.004   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 3150)
  covalent geometry    : angle       0.60726 ( 4292)
  SS BOND              : bond        0.00171 (    5)
  SS BOND              : angle       1.03046 (   10)
  hydrogen bonds       : bond        0.02980 (   94)
  hydrogen bonds       : angle       6.52078 (  225)
  link_NAG-ASN         : bond        0.00120 (    1)
  link_NAG-ASN         : angle       1.86318 (    3)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 35
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A  365 TYR cc_start: 0.7510 (m-80) cc_final: 0.6902 (m-80)
REVERT: A  493 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6772 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 40
  average time/residue: 0.0568
  time to fit residues: 2.8855
Evaluate side-chains
  43 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 33
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain A residue  489 TYR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  101 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:   20.0000
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0070
   chunk 11 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0670
   chunk 12 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0970
   overall best weight:    0.5736

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.071326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.064269 restraints weight = 14551.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.065742 restraints weight = 7574.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.066680 restraints weight = 4754.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.067307 restraints weight = 3398.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.067746 restraints weight = 2642.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   3156  Z= 0.099
  Angle     :  0.573   8.919   4305  Z= 0.294
  Chirality :  0.046   0.182    466
  Planarity :  0.004   0.065    562
  Dihedral  :  4.629  23.177    471
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 20.41 %
    Favored  : 76.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.61 (0.40), residues: 406
  helix: -2.60 (1.07), residues: 21
  sheet: -1.36 (0.40), residues: 165
  loop : -1.93 (0.41), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  98 
 TYR   0.011   0.001   TYR B  94 
 PHE   0.009   0.001   PHE A 456 
 TRP   0.009   0.001   TRP C  52 
 HIS   0.003   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 3150)
  covalent geometry    : angle       0.57215 ( 4292)
  SS BOND              : bond        0.00096 (    5)
  SS BOND              : angle       0.74195 (   10)
  hydrogen bonds       : bond        0.02660 (   94)
  hydrogen bonds       : angle       5.89934 (  225)
  link_NAG-ASN         : bond        0.00187 (    1)
  link_NAG-ASN         : angle       1.25460 (    3)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A  365 TYR cc_start: 0.7448 (m-80) cc_final: 0.6828 (m-80)
  outliers start: 8
  outliers final: 6
  residues processed: 42
  average time/residue: 0.0544
  time to fit residues: 2.9105
Evaluate side-chains
  41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain A residue  484 GLU
Chi-restraints excluded: chain A residue  489 TYR
Chi-restraints excluded: chain C residue  100 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 35 optimal weight:   20.0000
   chunk 12 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   chunk 24 optimal weight:    6.9990
   chunk 31 optimal weight:   20.0000
   chunk 19 optimal weight:    1.9990
   overall best weight:    2.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.070297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.062884 restraints weight = 14466.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.064327 restraints weight = 7726.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.065215 restraints weight = 4932.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.065857 restraints weight = 3618.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.066291 restraints weight = 2847.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3156  Z= 0.156
  Angle     :  0.612   7.992   4305  Z= 0.318
  Chirality :  0.047   0.167    466
  Planarity :  0.005   0.065    562
  Dihedral  :  4.991  21.984    471
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.39 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 19.73 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.58 (0.41), residues: 406
  helix: -2.56 (1.08), residues: 21
  sheet: -1.33 (0.40), residues: 163
  loop : -1.91 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 466 
 TYR   0.018   0.002   TYR B  94 
 PHE   0.010   0.001   PHE A 456 
 TRP   0.009   0.001   TRP C  52 
 HIS   0.004   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3150)
  covalent geometry    : angle       0.60892 ( 4292)
  SS BOND              : bond        0.00189 (    5)
  SS BOND              : angle       1.13418 (   10)
  hydrogen bonds       : bond        0.03025 (   94)
  hydrogen bonds       : angle       6.17559 (  225)
  link_NAG-ASN         : bond        0.00135 (    1)
  link_NAG-ASN         : angle       1.38938 (    3)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A  365 TYR cc_start: 0.7568 (m-80) cc_final: 0.6881 (m-80)
  outliers start: 9
  outliers final: 7
  residues processed: 37
  average time/residue: 0.0540
  time to fit residues: 2.6285
Evaluate side-chains
  37 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain A residue  484 GLU
Chi-restraints excluded: chain A residue  489 TYR
Chi-restraints excluded: chain B residue   19 VAL
Chi-restraints excluded: chain C residue  100 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 3 optimal weight:    7.9990
   chunk 20 optimal weight:    9.9990
   chunk 34 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0020
   chunk 35 optimal weight:    9.9990
   chunk 1 optimal weight:    2.9990
   chunk 37 optimal weight:   30.0000
   chunk 27 optimal weight:    0.9980
   overall best weight:    1.3392

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.070731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.063524 restraints weight = 14183.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.064943 restraints weight = 7579.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.065857 restraints weight = 4828.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.066447 restraints weight = 3472.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.066753 restraints weight = 2741.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.2460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3156  Z= 0.121
  Angle     :  0.601   8.484   4305  Z= 0.312
  Chirality :  0.046   0.178    466
  Planarity :  0.005   0.065    562
  Dihedral  :  4.816  23.068    471
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 19.05 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.55 (0.41), residues: 406
  helix: -2.87 (0.86), residues: 27
  sheet: -1.36 (0.40), residues: 166
  loop : -1.75 (0.42), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  98 
 TYR   0.015   0.001   TYR B  94 
 PHE   0.010   0.001   PHE A 456 
 TRP   0.009   0.001   TRP C  52 
 HIS   0.003   0.002   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 3150)
  covalent geometry    : angle       0.59914 ( 4292)
  SS BOND              : bond        0.00112 (    5)
  SS BOND              : angle       0.95979 (   10)
  hydrogen bonds       : bond        0.02834 (   94)
  hydrogen bonds       : angle       6.03296 (  225)
  link_NAG-ASN         : bond        0.00211 (    1)
  link_NAG-ASN         : angle       1.37950 (    3)

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

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

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  812 Ramachandran restraints generated.
    406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A  365 TYR cc_start: 0.7505 (m-80) cc_final: 0.6870 (m-80)
REVERT: A  493 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6818 (tm-30)
  outliers start: 9
  outliers final: 6
  residues processed: 40
  average time/residue: 0.0500
  time to fit residues: 2.5772
Evaluate side-chains
  41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain A residue  484 GLU
Chi-restraints excluded: chain A residue  489 TYR
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain C residue  100 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 35 optimal weight:   30.0000
   chunk 3 optimal weight:    0.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    1.1386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.071288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.063961 restraints weight = 14255.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.065366 restraints weight = 7616.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.066330 restraints weight = 4896.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.066918 restraints weight = 3528.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.067326 restraints weight = 2808.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.2600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3156  Z= 0.112
  Angle     :  0.597   8.475   4305  Z= 0.310
  Chirality :  0.046   0.177    466
  Planarity :  0.004   0.065    562
  Dihedral  :  4.731  25.521    471
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 19.05 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.46 (0.41), residues: 406
  helix: -2.74 (0.88), residues: 27
  sheet: -1.24 (0.41), residues: 156
  loop : -1.76 (0.41), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  98 
 TYR   0.014   0.001   TYR B  94 
 PHE   0.010   0.001   PHE A 515 
 TRP   0.009   0.001   TRP C  52 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 3150)
  covalent geometry    : angle       0.59521 ( 4292)
  SS BOND              : bond        0.00102 (    5)
  SS BOND              : angle       0.88209 (   10)
  hydrogen bonds       : bond        0.02831 (   94)
  hydrogen bonds       : angle       5.93934 (  225)
  link_NAG-ASN         : bond        0.00194 (    1)
  link_NAG-ASN         : angle       1.32342 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 689.28 seconds
wall clock time: 12 minutes 32.03 seconds (752.03 seconds total)