Starting phenix.real_space_refine
on Fri Aug 22 13:19:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bg6_16024/08_2025/8bg6_16024.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bg6_16024/08_2025/8bg6_16024.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bg6_16024/08_2025/8bg6_16024.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bg6_16024/08_2025/8bg6_16024.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bg6_16024/08_2025/8bg6_16024.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bg6_16024/08_2025/8bg6_16024.cif"
  }
  resolution = 4.11
  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
-------------------------------------------------------------------------------
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=   0.001 sd=   0.017
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      16      5.16       5
     C    1981      2.51       5
     N     527      2.21       5
     O     600      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3124
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 845
          Classifications: {'peptide': 110}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 105}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 815
          Classifications: {'peptide': 106}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "E"
      Number of atoms: 1450
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1450
          Classifications: {'peptide': 182}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 172}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "E"
      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: 0.79, per 1000 atoms: 0.25
  Number of scatterers: 3124
  At special positions: 0
  Unit cell: (66.64, 65.96, 94.52, 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      16     16.00
     O     600      8.00
     N     527      7.00
     C    1981      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=1.94
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " 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 E2000 " - " ASN E 343 "
  Time building additional restraints: 0.23
  Conformation dependent library (CDL) restraints added in 113.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  728

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 7 sheets defined
      8.3% alpha, 27.6% 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 86 through 90
      removed outlier: 3.596A  pdb=" N   THR A  90 " --> pdb=" O   PRO A  87 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 337 through 342
      removed outlier: 3.781A  pdb=" N   VAL E 341 " --> pdb=" O   PRO E 337 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 349 through 353
      removed outlier: 3.681A  pdb=" N   ALA E 352 " --> pdb=" O   SER E 349 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   TRP E 353 " --> pdb=" O   VAL E 350 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 349 through 353'
    Processing helix  chain 'E' and resid 384 through 388
      removed outlier: 3.579A  pdb=" N   LEU E 387 " --> pdb=" O   PRO E 384 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   ASN E 388 " --> pdb=" O   THR E 385 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 384 through 388'
    Processing helix  chain 'E' and resid 404 through 410
      removed outlier: 3.683A  pdb=" N   VAL E 407 " --> pdb=" O   GLY E 404 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ARG E 408 " --> pdb=" O   ASP E 405 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 502 through 506
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7
      removed outlier: 3.583A  pdb=" N   SER A  21 " --> pdb=" O   SER A   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11
      removed outlier: 6.072A  pdb=" N   GLY A  10 " --> pdb=" O   THR A 111 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   VAL A  37 " --> pdb=" O   TYR A  94 " (cutoff:3.500A)
      removed outlier: 5.675A  pdb=" N   ARG A  38 " --> pdb=" O   TRP A  47 " (cutoff:3.500A)
      removed outlier: 5.039A  pdb=" N   TRP A  47 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.524A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   GLN B  37 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
      removed outlier: 5.344A  pdb=" N   LEU B  46 " --> pdb=" O   GLN B  37 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   TYR B  49 " --> pdb=" O   HIS B  53 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   HIS B  53 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 24
    Processing sheet with id=AA5, first strand: chain 'E' and resid 355 through 358
      removed outlier: 7.161A  pdb=" N   ASN E 437 " --> pdb=" O   PHE E 374 " (cutoff:3.500A)
      removed outlier: 7.514A  pdb=" N   PHE E 374 " --> pdb=" O   ASN E 437 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 453
    Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474
      removed outlier: 3.500A  pdb=" N   TYR E 473 " --> pdb=" O   TYR E 489 " (cutoff:3.500A)

    85 hydrogen bonds defined for protein.
    198 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: 0.37

  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:
        1.21 -     1.33: 757
        1.33 -     1.45: 729
        1.45 -     1.57: 1696
        1.57 -     1.69: 0
        1.69 -     1.82: 20
  Bond restraints: 3202
  Sorted by residual:
  bond pdb=" N   SER A  31 "
       pdb=" CA  SER A  31 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.026 9.00e-03 1.23e+04 8.67e+00
  bond pdb=" N   ASN E 343 "
       pdb=" CA  ASN E 343 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.06e-02 8.90e+03 8.49e+00
  bond pdb=" N   GLU A  26 "
       pdb=" CA  GLU A  26 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.23e-02 6.61e+03 8.41e+00
  bond pdb=" N   VAL E 362 "
       pdb=" CA  VAL E 362 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.034 1.19e-02 7.06e+03 8.09e+00
  bond pdb=" N   TYR A  93 "
       pdb=" CA  TYR A  93 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.16e-02 7.43e+03 7.95e+00
  ... (remaining 3197 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 4044
        1.73 -     3.46: 254
        3.46 -     5.19: 44
        5.19 -     6.93: 7
        6.93 -     8.66: 3
  Bond angle restraints: 4352
  Sorted by residual:
  angle pdb=" CB  LYS E 386 "
        pdb=" CG  LYS E 386 "
        pdb=" CD  LYS E 386 "
      ideal   model   delta    sigma   weight residual
     111.30  119.96   -8.66 2.30e+00 1.89e-01 1.42e+01
  angle pdb=" CA  THR A 108 "
        pdb=" C   THR A 108 "
        pdb=" O   THR A 108 "
      ideal   model   delta    sigma   weight residual
     121.46  117.15    4.31 1.17e+00 7.31e-01 1.36e+01
  angle pdb=" CA  ILE A 103 "
        pdb=" C   ILE A 103 "
        pdb=" O   ILE A 103 "
      ideal   model   delta    sigma   weight residual
     120.25  116.69    3.56 9.90e-01 1.02e+00 1.29e+01
  angle pdb=" C   ILE A 103 "
        pdb=" N   TRP A 104 "
        pdb=" CA  TRP A 104 "
      ideal   model   delta    sigma   weight residual
     123.00  127.93   -4.93 1.38e+00 5.25e-01 1.28e+01
  angle pdb=" CA  GLN E 474 "
        pdb=" CB  GLN E 474 "
        pdb=" CG  GLN E 474 "
      ideal   model   delta    sigma   weight residual
     114.10  121.07   -6.97 2.00e+00 2.50e-01 1.21e+01
  ... (remaining 4347 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.98: 1706
       15.98 -    31.95: 144
       31.95 -    47.93: 39
       47.93 -    63.91: 5
       63.91 -    79.88: 2
  Dihedral angle restraints: 1896
    sinusoidal: 746
      harmonic: 1150
  Sorted by residual:
  dihedral pdb=" CB  CYS E 480 "
           pdb=" SG  CYS E 480 "
           pdb=" SG  CYS E 488 "
           pdb=" CB  CYS E 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.54  -68.54     1      1.00e+01 1.00e-02 6.09e+01
  dihedral pdb=" CA  GLY A 105 "
           pdb=" C   GLY A 105 "
           pdb=" N   GLN A 106 "
           pdb=" CA  GLN A 106 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.50  -18.50     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" C   SER A  31 "
           pdb=" N   SER A  31 "
           pdb=" CA  SER A  31 "
           pdb=" CB  SER A  31 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.69    9.09     0      2.50e+00 1.60e-01 1.32e+01
  ... (remaining 1893 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 377
       0.068 -    0.136: 75
       0.136 -    0.204: 15
       0.204 -    0.272: 0
       0.272 -    0.340: 2
  Chirality restraints: 469
  Sorted by residual:
  chirality pdb=" CA  ILE A 103 "
            pdb=" N   ILE A 103 "
            pdb=" C   ILE A 103 "
            pdb=" CB  ILE A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.77   -0.34 2.00e-01 2.50e+01 2.89e+00
  chirality pdb=" CA  SER A  31 "
            pdb=" N   SER A  31 "
            pdb=" C   SER A  31 "
            pdb=" CB  SER A  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.33 2.00e-01 2.50e+01 2.65e+00
  chirality pdb=" CA  ASN A  76 "
            pdb=" N   ASN A  76 "
            pdb=" C   ASN A  76 "
            pdb=" CB  ASN A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.86e-01
  ... (remaining 466 not shown)

  Planarity restraints: 566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  40 "   -0.042 5.00e-02 4.00e+02   6.32e-02 6.40e+00
        pdb=" N   PRO A  41 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A  41 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A  41 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A  96 "    0.011 2.00e-02 2.50e+03   2.27e-02 5.16e+00
        pdb=" C   ALA A  96 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ALA A  96 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ARG A  97 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  16 "   -0.009 2.00e-02 2.50e+03   1.90e-02 3.62e+00
        pdb=" C   GLY A  16 "    0.033 2.00e-02 2.50e+03
        pdb=" O   GLY A  16 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   SER A  17 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 563 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 1161
        2.86 -     3.37: 2456
        3.37 -     3.88: 4514
        3.88 -     4.39: 4882
        4.39 -     4.90: 8948
  Nonbonded interactions: 21961
  Sorted by model distance:
  nonbonded pdb=" O   ASP B  28 "
            pdb=" OD1 ASP B  28 "
     model   vdw
     2.348 3.040
  nonbonded pdb=" O   MET A  99 "
            pdb=" CG  ARG A 100 "
     model   vdw
     2.425 3.440
  nonbonded pdb=" OE1 GLU A 102 "
            pdb=" OH  TYR B  36 "
     model   vdw
     2.463 3.040
  nonbonded pdb=" OD1 ASN E 448 "
            pdb=" N   ASN E 450 "
     model   vdw
     2.473 3.120
  nonbonded pdb=" O   SER E 366 "
            pdb=" N   TYR E 369 "
     model   vdw
     2.496 3.120
  ... (remaining 21956 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:             1.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.250
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
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      :  0.006   0.088   3207  Z= 0.418
  Angle     :  0.953   9.554   4363  Z= 0.608
  Chirality :  0.060   0.340    469
  Planarity :  0.005   0.068    565
  Dihedral  : 12.582  79.885   1156
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.89 %
    Favored  : 93.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.14 %
    Favored  : 90.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.90 (0.43), residues: 392
  helix: -3.56 (0.97), residues: 18
  sheet:  0.73 (0.50), residues: 116
  loop : -1.06 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  61 
 TYR   0.014   0.001   TYR E 473 
 PHE   0.011   0.001   PHE E 400 
 TRP   0.009   0.001   TRP E 436 
 HIS   0.006   0.002   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00602 ( 3202)
  covalent geometry    : angle       0.93687 ( 4352)
  SS BOND              : bond        0.04397 (    4)
  SS BOND              : angle       3.69740 (    8)
  hydrogen bonds       : bond        0.22035 (   85)
  hydrogen bonds       : angle       6.05639 (  198)
  link_NAG-ASN         : bond        0.04698 (    1)
  link_NAG-ASN         : angle       3.35730 (    3)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0565
  time to fit residues: 5.5755
Evaluate side-chains
  61 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 26 optimal weight:    0.0970
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0470
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    0.0670
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.3414

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

Flipped N/Q/H residues before XYZ refinement:
A 101 HIS
B  34 ASN
** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.147498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.119064 restraints weight = 4379.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.118243 restraints weight = 5825.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.119198 restraints weight = 5282.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.119417 restraints weight = 4363.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.119587 restraints weight = 4081.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3207  Z= 0.105
  Angle     :  0.551   5.183   4363  Z= 0.293
  Chirality :  0.044   0.134    469
  Planarity :  0.004   0.034    565
  Dihedral  :  4.022  14.810    461
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.44), residues: 392
  helix: -3.41 (0.95), residues: 18
  sheet:  0.66 (0.51), residues: 123
  loop : -0.38 (0.41), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 509 
 TYR   0.014   0.001   TYR E 453 
 PHE   0.009   0.001   PHE B  32 
 TRP   0.011   0.001   TRP E 436 
 HIS   0.004   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 3202)
  covalent geometry    : angle       0.54898 ( 4352)
  SS BOND              : bond        0.00447 (    4)
  SS BOND              : angle       1.13079 (    8)
  hydrogen bonds       : bond        0.03947 (   85)
  hydrogen bonds       : angle       5.05802 (  198)
  link_NAG-ASN         : bond        0.00313 (    1)
  link_NAG-ASN         : angle       0.71724 (    3)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
REVERT: A   88 GLU cc_start: 0.7329 (tp30) cc_final: 0.7013 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0569
  time to fit residues: 5.6870
Evaluate side-chains
  63 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0570
   chunk 9 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 37 optimal weight:    0.2980
   overall best weight:    0.5700

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

Flipped N/Q/H residues before XYZ refinement:
** E 506 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 = 0.3609 r_free = 0.3609 target = 0.149085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.137588 restraints weight = 4329.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.129874 restraints weight = 7348.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.124434 restraints weight = 5667.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.124845 restraints weight = 7433.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.125460 restraints weight = 5229.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3207  Z= 0.108
  Angle     :  0.533   4.915   4363  Z= 0.284
  Chirality :  0.044   0.132    469
  Planarity :  0.004   0.036    565
  Dihedral  :  3.877  13.724    461
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.44), residues: 392
  helix: -3.30 (0.98), residues: 18
  sheet:  0.63 (0.50), residues: 126
  loop : -0.11 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  18 
 TYR   0.010   0.001   TYR B  49 
 PHE   0.011   0.001   PHE B  73 
 TRP   0.024   0.002   TRP A  36 
 HIS   0.002   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 3202)
  covalent geometry    : angle       0.53213 ( 4352)
  SS BOND              : bond        0.00588 (    4)
  SS BOND              : angle       0.97459 (    8)
  hydrogen bonds       : bond        0.03805 (   85)
  hydrogen bonds       : angle       4.90213 (  198)
  link_NAG-ASN         : bond        0.00272 (    1)
  link_NAG-ASN         : angle       0.74884 (    3)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.072 
Fit side-chains
REVERT: A   88 GLU cc_start: 0.7427 (tp30) cc_final: 0.7222 (tp30)
REVERT: B   79 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8432 (mp10)
REVERT: E  370 ASN cc_start: 0.8452 (p0) cc_final: 0.8240 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.0498
  time to fit residues: 4.9049
Evaluate side-chains
  70 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 36 optimal weight:   10.0000
   chunk 35 optimal weight:    8.9990
   chunk 3 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0770
   chunk 21 optimal weight:    0.0470
   chunk 24 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    1.4040

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

Flipped N/Q/H residues before XYZ refinement:
E 439 ASN
** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.136130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.123930 restraints weight = 4499.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.113488 restraints weight = 8464.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.108830 restraints weight = 6845.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.109868 restraints weight = 7755.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.108223 restraints weight = 7305.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.3101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3207  Z= 0.167
  Angle     :  0.596   4.958   4363  Z= 0.322
  Chirality :  0.046   0.176    469
  Planarity :  0.004   0.040    565
  Dihedral  :  4.213  14.864    461
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  1.77 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.43), residues: 392
  helix: -2.89 (0.83), residues: 30
  sheet:  0.64 (0.49), residues: 130
  loop : -0.25 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 357 
 TYR   0.013   0.002   TYR B  36 
 PHE   0.011   0.001   PHE B  73 
 TRP   0.036   0.003   TRP A  36 
 HIS   0.002   0.001   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 3202)
  covalent geometry    : angle       0.59356 ( 4352)
  SS BOND              : bond        0.00847 (    4)
  SS BOND              : angle       1.29743 (    8)
  hydrogen bonds       : bond        0.04413 (   85)
  hydrogen bonds       : angle       5.31811 (  198)
  link_NAG-ASN         : bond        0.00116 (    1)
  link_NAG-ASN         : angle       0.99968 (    3)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.086 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 ASP cc_start: 0.8449 (t0) cc_final: 0.8100 (t0)
REVERT: A  106 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7928 (mm-40)
REVERT: E  370 ASN cc_start: 0.8620 (p0) cc_final: 0.8414 (p0)
REVERT: E  400 PHE cc_start: 0.7666 (m-80) cc_final: 0.7461 (m-80)
REVERT: E  465 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7633 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0612
  time to fit residues: 6.1021
Evaluate side-chains
  71 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0970
   chunk 29 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** E 506 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 = 0.3575 r_free = 0.3575 target = 0.146043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.134918 restraints weight = 4260.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.135629 restraints weight = 7774.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.134449 restraints weight = 5633.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.134254 restraints weight = 5029.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.134362 restraints weight = 4216.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.3251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3207  Z= 0.112
  Angle     :  0.540   4.946   4363  Z= 0.285
  Chirality :  0.044   0.129    469
  Planarity :  0.004   0.044    565
  Dihedral  :  3.946  13.392    461
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.43), residues: 392
  helix: -3.15 (0.90), residues: 24
  sheet:  0.72 (0.49), residues: 128
  loop : -0.12 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 509 
 TYR   0.011   0.001   TYR B  36 
 PHE   0.010   0.001   PHE B  73 
 TRP   0.025   0.002   TRP A  36 
 HIS   0.004   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 3202)
  covalent geometry    : angle       0.53867 ( 4352)
  SS BOND              : bond        0.00567 (    4)
  SS BOND              : angle       0.85812 (    8)
  hydrogen bonds       : bond        0.03565 (   85)
  hydrogen bonds       : angle       4.96856 (  198)
  link_NAG-ASN         : bond        0.00209 (    1)
  link_NAG-ASN         : angle       0.82645 (    3)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
REVERT: A  106 GLN cc_start: 0.7956 (tp-100) cc_final: 0.7740 (mm-40)
REVERT: E  370 ASN cc_start: 0.6935 (p0) cc_final: 0.6732 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.0631
  time to fit residues: 5.8676
Evaluate side-chains
  67 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0050
   chunk 6 optimal weight:    0.4980
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    8.9990
   chunk 31 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    1.0798

-------------------------------------------------------------------------------
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 = 0.3531 r_free = 0.3531 target = 0.142595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.130508 restraints weight = 4406.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.125209 restraints weight = 8874.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.122670 restraints weight = 7084.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.122064 restraints weight = 7654.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.122110 restraints weight = 5783.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3207  Z= 0.139
  Angle     :  0.572   4.749   4363  Z= 0.305
  Chirality :  0.045   0.135    469
  Planarity :  0.004   0.044    565
  Dihedral  :  4.022  13.618    461
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.44), residues: 392
  helix: -3.12 (0.90), residues: 24
  sheet:  0.75 (0.48), residues: 134
  loop : -0.09 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 357 
 TYR   0.010   0.001   TYR E 453 
 PHE   0.011   0.001   PHE B  73 
 TRP   0.037   0.002   TRP A  36 
 HIS   0.004   0.002   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3202)
  covalent geometry    : angle       0.57072 ( 4352)
  SS BOND              : bond        0.00701 (    4)
  SS BOND              : angle       1.06699 (    8)
  hydrogen bonds       : bond        0.03916 (   85)
  hydrogen bonds       : angle       5.05973 (  198)
  link_NAG-ASN         : bond        0.00150 (    1)
  link_NAG-ASN         : angle       0.92282 (    3)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.073 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 ASP cc_start: 0.8201 (t0) cc_final: 0.7954 (t0)
REVERT: A  106 GLN cc_start: 0.8138 (tp-100) cc_final: 0.7904 (mm-40)
REVERT: E  370 ASN cc_start: 0.7753 (p0) cc_final: 0.7488 (p0)
REVERT: E  465 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7393 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.0734
  time to fit residues: 6.4651
Evaluate side-chains
  65 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 34 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 35 optimal weight:    9.9990
   chunk 16 optimal weight:    0.2980
   chunk 18 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   chunk 7 optimal weight:    0.4980
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.3523 r_free = 0.3523 target = 0.141563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.128637 restraints weight = 4518.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.121094 restraints weight = 8496.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.116112 restraints weight = 7781.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.116756 restraints weight = 8532.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.117130 restraints weight = 5847.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.3548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3207  Z= 0.146
  Angle     :  0.576   4.353   4363  Z= 0.308
  Chirality :  0.046   0.147    469
  Planarity :  0.004   0.044    565
  Dihedral  :  4.056  14.837    461
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.44), residues: 392
  helix: -3.22 (0.86), residues: 24
  sheet:  0.48 (0.44), residues: 154
  loop : -0.02 (0.44), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  18 
 TYR   0.011   0.001   TYR B  96 
 PHE   0.011   0.001   PHE B  73 
 TRP   0.046   0.003   TRP A  36 
 HIS   0.003   0.002   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 3202)
  covalent geometry    : angle       0.57442 ( 4352)
  SS BOND              : bond        0.00676 (    4)
  SS BOND              : angle       1.00255 (    8)
  hydrogen bonds       : bond        0.04021 (   85)
  hydrogen bonds       : angle       5.24757 (  198)
  link_NAG-ASN         : bond        0.00137 (    1)
  link_NAG-ASN         : angle       0.91746 (    3)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 ASP cc_start: 0.8378 (t0) cc_final: 0.8070 (t0)
REVERT: A  106 GLN cc_start: 0.8136 (tp-100) cc_final: 0.7871 (mm-40)
REVERT: E  370 ASN cc_start: 0.8266 (p0) cc_final: 0.8027 (p0)
REVERT: E  400 PHE cc_start: 0.7698 (m-80) cc_final: 0.7359 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0709
  time to fit residues: 6.3119
Evaluate side-chains
  58 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 26 optimal weight:    7.9990
   chunk 4 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 0 optimal weight:    0.7980
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.3473 r_free = 0.3473 target = 0.137621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.124884 restraints weight = 4485.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.124461 restraints weight = 8357.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.124235 restraints weight = 6744.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.123733 restraints weight = 5731.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.123959 restraints weight = 5039.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.3631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3207  Z= 0.127
  Angle     :  0.585   6.251   4363  Z= 0.308
  Chirality :  0.045   0.135    469
  Planarity :  0.004   0.047    565
  Dihedral  :  3.965  14.116    461
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.44), residues: 392
  helix: -3.19 (0.87), residues: 24
  sheet:  0.53 (0.45), residues: 153
  loop : -0.02 (0.44), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 357 
 TYR   0.009   0.001   TYR B  36 
 PHE   0.011   0.001   PHE B  73 
 TRP   0.040   0.002   TRP A  36 
 HIS   0.003   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3202)
  covalent geometry    : angle       0.58382 ( 4352)
  SS BOND              : bond        0.00585 (    4)
  SS BOND              : angle       0.88980 (    8)
  hydrogen bonds       : bond        0.03893 (   85)
  hydrogen bonds       : angle       5.15832 (  198)
  link_NAG-ASN         : bond        0.00173 (    1)
  link_NAG-ASN         : angle       0.86598 (    3)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
REVERT: A  106 GLN cc_start: 0.8119 (tp-100) cc_final: 0.7828 (mm-40)
REVERT: E  370 ASN cc_start: 0.7081 (p0) cc_final: 0.6835 (p0)
REVERT: E  400 PHE cc_start: 0.7700 (m-80) cc_final: 0.7355 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.0683
  time to fit residues: 5.9399
Evaluate side-chains
  60 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 25 optimal weight:    5.9990
   chunk 18 optimal weight:    0.3980
   chunk 19 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3555 r_free = 0.3555 target = 0.144037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.132527 restraints weight = 4399.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.125561 restraints weight = 7913.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.119511 restraints weight = 6370.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.119741 restraints weight = 8678.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.120109 restraints weight = 6831.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.3750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3207  Z= 0.125
  Angle     :  0.589   4.622   4363  Z= 0.313
  Chirality :  0.045   0.136    469
  Planarity :  0.004   0.049    565
  Dihedral  :  4.010  14.667    461
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.44), residues: 392
  helix: -3.24 (0.85), residues: 24
  sheet:  0.52 (0.45), residues: 153
  loop : -0.00 (0.44), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 357 
 TYR   0.009   0.001   TYR E 453 
 PHE   0.011   0.001   PHE B  73 
 TRP   0.044   0.002   TRP A  36 
 HIS   0.003   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 3202)
  covalent geometry    : angle       0.58781 ( 4352)
  SS BOND              : bond        0.00559 (    4)
  SS BOND              : angle       0.86165 (    8)
  hydrogen bonds       : bond        0.03782 (   85)
  hydrogen bonds       : angle       5.09338 (  198)
  link_NAG-ASN         : bond        0.00144 (    1)
  link_NAG-ASN         : angle       0.84129 (    3)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 ASP cc_start: 0.8284 (t0) cc_final: 0.8035 (t0)
REVERT: A  106 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7865 (mm-40)
REVERT: E  370 ASN cc_start: 0.8040 (p0) cc_final: 0.7785 (p0)
REVERT: E  474 GLN cc_start: 0.7774 (pp30) cc_final: 0.7458 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0706
  time to fit residues: 6.2117
Evaluate side-chains
  63 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 35 optimal weight:    8.9990
   chunk 24 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0870
   chunk 29 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** E 506 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 = 0.3542 r_free = 0.3542 target = 0.143160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.130969 restraints weight = 4404.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.123106 restraints weight = 8378.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.118900 restraints weight = 6616.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.119494 restraints weight = 6832.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.119943 restraints weight = 4907.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.3738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3207  Z= 0.117
  Angle     :  0.583   4.731   4363  Z= 0.309
  Chirality :  0.045   0.130    469
  Planarity :  0.004   0.050    565
  Dihedral  :  3.899  14.158    461
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.44), residues: 392
  helix: -3.16 (0.86), residues: 24
  sheet:  0.70 (0.47), residues: 144
  loop : -0.01 (0.43), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 357 
 TYR   0.009   0.001   TYR B  36 
 PHE   0.011   0.001   PHE B  73 
 TRP   0.014   0.001   TRP A  36 
 HIS   0.003   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 3202)
  covalent geometry    : angle       0.58255 ( 4352)
  SS BOND              : bond        0.00535 (    4)
  SS BOND              : angle       0.77143 (    8)
  hydrogen bonds       : bond        0.03771 (   85)
  hydrogen bonds       : angle       5.11252 (  198)
  link_NAG-ASN         : bond        0.00158 (    1)
  link_NAG-ASN         : angle       0.81617 (    3)

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

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

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  784 Ramachandran restraints generated.
    392 Oldfield, 0 Emsley, 392 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 ASP cc_start: 0.8252 (t0) cc_final: 0.7944 (t0)
REVERT: E  370 ASN cc_start: 0.8319 (p0) cc_final: 0.8086 (p0)
REVERT: E  474 GLN cc_start: 0.7755 (pp30) cc_final: 0.7463 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.0882
  time to fit residues: 7.4026
Evaluate side-chains
  61 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 38 optimal weight:    0.4980
   chunk 15 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0670
   chunk 33 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
** E 506 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 = 0.3489 r_free = 0.3489 target = 0.138985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.126987 restraints weight = 4380.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.126166 restraints weight = 8294.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.125627 restraints weight = 7599.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.125267 restraints weight = 5580.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.125434 restraints weight = 5020.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.3832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3207  Z= 0.112
  Angle     :  0.569   5.076   4363  Z= 0.302
  Chirality :  0.044   0.129    469
  Planarity :  0.004   0.050    565
  Dihedral  :  3.832  13.873    461
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.44), residues: 392
  helix: -3.19 (0.83), residues: 24
  sheet:  0.73 (0.46), residues: 143
  loop : -0.06 (0.42), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 357 
 TYR   0.008   0.001   TYR B  36 
 PHE   0.012   0.001   PHE B  73 
 TRP   0.015   0.001   TRP A  36 
 HIS   0.003   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 3202)
  covalent geometry    : angle       0.56804 ( 4352)
  SS BOND              : bond        0.00522 (    4)
  SS BOND              : angle       0.77781 (    8)
  hydrogen bonds       : bond        0.03583 (   85)
  hydrogen bonds       : angle       4.97489 (  198)
  link_NAG-ASN         : bond        0.00155 (    1)
  link_NAG-ASN         : angle       0.80383 (    3)

===============================================================================
Job complete
usr+sys time: 702.75 seconds
wall clock time: 12 minutes 40.70 seconds (760.70 seconds total)