Starting phenix.real_space_refine
on Wed Mar  4 03:31:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s9d_24933/03_2026/7s9d_24933.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s9d_24933/03_2026/7s9d_24933.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s9d_24933/03_2026/7s9d_24933.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s9d_24933/03_2026/7s9d_24933.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s9d_24933/03_2026/7s9d_24933.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s9d_24933/03_2026/7s9d_24933.map"
  }
  resolution = 4.6
  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=   0.003
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      50      5.16       5
     C    6860      2.51       5
     N    1682      2.21       5
     O    1870      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 10462
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 677, 5231
          Classifications: {'peptide': 677}
          Link IDs: {'PTRANS': 33, 'TRANS': 643}
          Chain breaks: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.98, per 1000 atoms: 0.38
  Number of scatterers: 10462
  At special positions: 0
  Unit cell: (115.867, 111.615, 112.678, 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      50     16.00
     O    1870      8.00
     N    1682      7.00
     C    6860      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 536.7 milliseconds
  

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2500

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 2 sheets defined
      61.9% alpha, 1.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 32
    Processing helix  chain 'A' and resid 53 through 65
    Processing helix  chain 'A' and resid 66 through 70
    Processing helix  chain 'A' and resid 77 through 105
      Proline residue:  A  96  - end of helix
    Processing helix  chain 'A' and resid 108 through 126
      removed outlier: 4.176A  pdb=" N   GLY A 112 " --> pdb=" O   PRO A 108 " (cutoff:3.500A)
      Proline residue:  A 119  - end of helix
    Processing helix  chain 'A' and resid 137 through 151
      removed outlier: 3.612A  pdb=" N   SER A 141 " --> pdb=" O   PHE A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 196
    Processing helix  chain 'A' and resid 199 through 205
      removed outlier: 4.124A  pdb=" N   LEU A 205 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 228
      removed outlier: 3.718A  pdb=" N   VAL A 210 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 253
      removed outlier: 3.541A  pdb=" N   ASN A 253 " --> pdb=" O   ALA A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 282
      removed outlier: 3.867A  pdb=" N   PHE A 282 " --> pdb=" O   PHE A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 306
      removed outlier: 3.790A  pdb=" N   VAL A 297 " --> pdb=" O   GLU A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 363
    Processing helix  chain 'A' and resid 370 through 388
    Processing helix  chain 'A' and resid 398 through 406
    Processing helix  chain 'A' and resid 411 through 428
    Processing helix  chain 'A' and resid 429 through 433
      removed outlier: 3.563A  pdb=" N   PHE A 432 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 453
    Processing helix  chain 'A' and resid 457 through 465
    Processing helix  chain 'A' and resid 465 through 482
      removed outlier: 3.759A  pdb=" N   LEU A 469 " --> pdb=" O   SER A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 503
    Processing helix  chain 'A' and resid 549 through 561
    Processing helix  chain 'A' and resid 563 through 581
      removed outlier: 3.514A  pdb=" N   LYS A 580 " --> pdb=" O   LYS A 576 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   GLU A 581 " --> pdb=" O   LYS A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 671
    Processing helix  chain 'A' and resid 681 through 690
    Processing helix  chain 'A' and resid 698 through 700
      No H-bonds generated for 'chain 'A' and resid 698 through 700'
    Processing helix  chain 'A' and resid 705 through 721
    Processing helix  chain 'B' and resid 25 through 32
    Processing helix  chain 'B' and resid 53 through 65
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 77 through 105
      Proline residue:  B  96  - end of helix
    Processing helix  chain 'B' and resid 108 through 126
      removed outlier: 4.177A  pdb=" N   GLY B 112 " --> pdb=" O   PRO B 108 " (cutoff:3.500A)
      Proline residue:  B 119  - end of helix
    Processing helix  chain 'B' and resid 137 through 151
      removed outlier: 3.611A  pdb=" N   SER B 141 " --> pdb=" O   PHE B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 196
    Processing helix  chain 'B' and resid 199 through 205
      removed outlier: 4.125A  pdb=" N   LEU B 205 " --> pdb=" O   VAL B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 228
      removed outlier: 3.716A  pdb=" N   VAL B 210 " --> pdb=" O   THR B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 253
      removed outlier: 3.542A  pdb=" N   ASN B 253 " --> pdb=" O   ALA B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 282
      removed outlier: 3.868A  pdb=" N   PHE B 282 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 306
      removed outlier: 3.791A  pdb=" N   VAL B 297 " --> pdb=" O   GLU B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 363
    Processing helix  chain 'B' and resid 370 through 388
    Processing helix  chain 'B' and resid 398 through 406
    Processing helix  chain 'B' and resid 411 through 428
    Processing helix  chain 'B' and resid 429 through 433
      removed outlier: 3.564A  pdb=" N   PHE B 432 " --> pdb=" O   GLY B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 453
    Processing helix  chain 'B' and resid 457 through 465
    Processing helix  chain 'B' and resid 465 through 482
      removed outlier: 3.759A  pdb=" N   LEU B 469 " --> pdb=" O   SER B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 503
    Processing helix  chain 'B' and resid 549 through 561
    Processing helix  chain 'B' and resid 563 through 581
      removed outlier: 3.514A  pdb=" N   LYS B 580 " --> pdb=" O   LYS B 576 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   GLU B 581 " --> pdb=" O   LYS B 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 653 through 671
    Processing helix  chain 'B' and resid 681 through 690
    Processing helix  chain 'B' and resid 698 through 700
      No H-bonds generated for 'chain 'B' and resid 698 through 700'
    Processing helix  chain 'B' and resid 705 through 721
    Processing sheet with id=AA1, first strand: chain 'A' and resid 535 through 539
      removed outlier: 6.230A  pdb=" N   ILE A 642 " --> pdb=" O   TYR A 675 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   ALA A 677 " --> pdb=" O   ILE A 642 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   LEU A 644 " --> pdb=" O   ALA A 677 " (cutoff:3.500A)
      removed outlier: 8.435A  pdb=" N   PHE A 703 " --> pdb=" O   VAL A 674 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   LEU A 676 " --> pdb=" O   PHE A 703 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 535 through 539
      removed outlier: 6.230A  pdb=" N   ILE B 642 " --> pdb=" O   TYR B 675 " (cutoff:3.500A)
      removed outlier: 7.607A  pdb=" N   ALA B 677 " --> pdb=" O   ILE B 642 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   LEU B 644 " --> pdb=" O   ALA B 677 " (cutoff:3.500A)
      removed outlier: 8.436A  pdb=" N   PHE B 703 " --> pdb=" O   VAL B 674 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   LEU B 676 " --> pdb=" O   PHE B 703 " (cutoff:3.500A)

    602 hydrogen bonds defined for protein.
    1788 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: 1.56

  Time building geometry restraints manager: 1.21 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: 3240
        1.34 -     1.46: 2515
        1.46 -     1.58: 4861
        1.58 -     1.70: 0
        1.70 -     1.82: 82
  Bond restraints: 10698
  Sorted by residual:
  bond pdb=" CA  SER B 400 "
       pdb=" CB  SER B 400 "
    ideal  model  delta    sigma   weight residual
    1.528  1.478  0.050 1.56e-02 4.11e+03 1.05e+01
  bond pdb=" CA  SER A 400 "
       pdb=" CB  SER A 400 "
    ideal  model  delta    sigma   weight residual
    1.528  1.478  0.050 1.56e-02 4.11e+03 1.04e+01
  bond pdb=" N   PHE A 137 "
       pdb=" CA  PHE A 137 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.19e-02 7.06e+03 7.05e+00
  bond pdb=" N   PHE B 137 "
       pdb=" CA  PHE B 137 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.19e-02 7.06e+03 6.96e+00
  bond pdb=" N   VAL A 139 "
       pdb=" CA  VAL A 139 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.029 1.24e-02 6.50e+03 5.42e+00
  ... (remaining 10693 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.94: 14339
        2.94 -     5.88: 185
        5.88 -     8.82: 10
        8.82 -    11.76: 4
       11.76 -    14.70: 2
  Bond angle restraints: 14540
  Sorted by residual:
  angle pdb=" N   LEU B 397 "
        pdb=" CA  LEU B 397 "
        pdb=" C   LEU B 397 "
      ideal   model   delta    sigma   weight residual
     113.88  106.31    7.57 1.23e+00 6.61e-01 3.78e+01
  angle pdb=" N   LEU A 397 "
        pdb=" CA  LEU A 397 "
        pdb=" C   LEU A 397 "
      ideal   model   delta    sigma   weight residual
     113.88  106.33    7.55 1.23e+00 6.61e-01 3.77e+01
  angle pdb=" C   PHE A  23 "
        pdb=" N   SER A  24 "
        pdb=" CA  SER A  24 "
      ideal   model   delta    sigma   weight residual
     121.54  112.05    9.49 1.91e+00 2.74e-01 2.47e+01
  angle pdb=" C   PHE B  23 "
        pdb=" N   SER B  24 "
        pdb=" CA  SER B  24 "
      ideal   model   delta    sigma   weight residual
     121.54  112.05    9.49 1.91e+00 2.74e-01 2.47e+01
  angle pdb=" CB  MET B 180 "
        pdb=" CG  MET B 180 "
        pdb=" SD  MET B 180 "
      ideal   model   delta    sigma   weight residual
     112.70   98.00   14.70 3.00e+00 1.11e-01 2.40e+01
  ... (remaining 14535 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.57: 5572
       12.57 -    25.14: 582
       25.14 -    37.71: 148
       37.71 -    50.28: 30
       50.28 -    62.84: 6
  Dihedral angle restraints: 6338
    sinusoidal: 2432
      harmonic: 3906
  Sorted by residual:
  dihedral pdb=" CA  SER A  24 "
           pdb=" C   SER A  24 "
           pdb=" N   HIS A  25 "
           pdb=" CA  HIS A  25 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.95   28.05     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CA  SER B  24 "
           pdb=" C   SER B  24 "
           pdb=" N   HIS B  25 "
           pdb=" CA  HIS B  25 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.06   27.94     0      5.00e+00 4.00e-02 3.12e+01
  dihedral pdb=" CA  TYR A 616 "
           pdb=" C   TYR A 616 "
           pdb=" N   PRO A 617 "
           pdb=" CA  PRO A 617 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.64   17.36     0      5.00e+00 4.00e-02 1.21e+01
  ... (remaining 6335 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1079
       0.039 -    0.077: 462
       0.077 -    0.115: 155
       0.115 -    0.154: 20
       0.154 -    0.192: 10
  Chirality restraints: 1726
  Sorted by residual:
  chirality pdb=" CA  LEU A 397 "
            pdb=" N   LEU A 397 "
            pdb=" C   LEU A 397 "
            pdb=" CB  LEU A 397 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.26e-01
  chirality pdb=" CA  LEU B 397 "
            pdb=" N   LEU B 397 "
            pdb=" C   LEU B 397 "
            pdb=" CB  LEU B 397 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.13e-01
  chirality pdb=" CG  LEU A  28 "
            pdb=" CB  LEU A  28 "
            pdb=" CD1 LEU A  28 "
            pdb=" CD2 LEU A  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.06e-01
  ... (remaining 1723 not shown)

  Planarity restraints: 1812
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 136 "    0.009 2.00e-02 2.50e+03   1.84e-02 3.39e+00
        pdb=" C   PRO A 136 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   PRO A 136 "    0.012 2.00e-02 2.50e+03
        pdb=" N   PHE A 137 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 136 "    0.009 2.00e-02 2.50e+03   1.76e-02 3.10e+00
        pdb=" C   PRO B 136 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   PRO B 136 "    0.012 2.00e-02 2.50e+03
        pdb=" N   PHE B 137 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 394 "   -0.008 2.00e-02 2.50e+03   1.63e-02 2.66e+00
        pdb=" C   SER A 394 "    0.028 2.00e-02 2.50e+03
        pdb=" O   SER A 394 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   CYS A 395 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1809 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 282
        2.66 -     3.22: 11872
        3.22 -     3.78: 17632
        3.78 -     4.34: 22681
        4.34 -     4.90: 34822
  Nonbonded interactions: 87289
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 227 "
            pdb=" OG1 THR A 234 "
     model   vdw
     2.095 3.120
  nonbonded pdb=" NZ  LYS B 227 "
            pdb=" OG1 THR B 234 "
     model   vdw
     2.096 3.120
  nonbonded pdb=" O   THR A 234 "
            pdb=" NH1 ARG A 236 "
     model   vdw
     2.100 3.120
  nonbonded pdb=" O   THR B 234 "
            pdb=" NH1 ARG B 236 "
     model   vdw
     2.100 3.120
  nonbonded pdb=" O   PHE A 460 "
            pdb=" OG1 THR A 464 "
     model   vdw
     2.103 3.040
  ... (remaining 87284 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
Set refine NCS operators
  NCS operators will be refined.
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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.150
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
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   0.051  10698  Z= 0.336
  Angle     :  0.888  14.704  14540  Z= 0.522
  Chirality :  0.047   0.192   1726
  Planarity :  0.005   0.039   1812
  Dihedral  : 11.266  62.844   3838
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 23.25
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 10.70 %
    Favored  : 89.00 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  0.96 %
    Favored  : 98.70 %
  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: -0.95 (0.23), residues: 1346
  helix:  0.66 (0.18), residues: 828
  sheet:  1.65 (0.83), residues: 38
  loop : -3.27 (0.25), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 281 
 TYR   0.013   0.002   TYR B 118 
 PHE   0.016   0.002   PHE A 213 
 TRP   0.024   0.003   TRP B 472 
 HIS   0.016   0.003   HIS A  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00639 (10698)
  covalent geometry    : angle       0.88785 (14540)
  hydrogen bonds       : bond        0.12419 (  602)
  hydrogen bonds       : angle       5.98100 ( 1788)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 0.144 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 32
  average time/residue: 0.0548
  time to fit residues: 2.6095
Evaluate side-chains
  26 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.2980
   chunk 124 optimal weight:    0.0030
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    0.0980
   chunk 55 optimal weight:    0.2980
   overall best weight:    0.2590
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 447 ASN
A 650 ASN
A 689 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.051333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.040491 restraints weight = 44800.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.041487 restraints weight = 27055.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.042218 restraints weight = 18579.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.042705 restraints weight = 14237.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.042985 restraints weight = 11738.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10698  Z= 0.135
  Angle     :  0.624   8.605  14540  Z= 0.316
  Chirality :  0.045   0.200   1726
  Planarity :  0.004   0.026   1812
  Dihedral  :  4.596  30.377   1448
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.58 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  5.91 %
    Favored  : 93.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.23), residues: 1346
  helix:  1.08 (0.18), residues: 832
  sheet:  2.58 (0.81), residues: 36
  loop : -3.16 (0.25), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 399 
 TYR   0.011   0.001   TYR A 123 
 PHE   0.014   0.001   PHE A  23 
 TRP   0.009   0.001   TRP A 472 
 HIS   0.009   0.001   HIS A  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (10698)
  covalent geometry    : angle       0.62400 (14540)
  hydrogen bonds       : bond        0.03962 (  602)
  hydrogen bonds       : angle       4.47909 ( 1788)

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: A  299 MET cc_start: 0.5853 (tpt) cc_final: 0.5490 (tpp)
REVERT: A  357 MET cc_start: 0.8716 (tpt) cc_final: 0.8151 (tpp)
REVERT: A  575 MET cc_start: 0.9172 (mmt) cc_final: 0.8836 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0452
  time to fit residues: 2.8122
Evaluate side-chains
  28 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0270
   chunk 58 optimal weight:    0.6980
   chunk 55 optimal weight:    8.9990
   chunk 131 optimal weight:   10.0000
   chunk 102 optimal weight:   20.0000
   chunk 124 optimal weight:    0.9990
   chunk 57 optimal weight:    6.9990
   chunk 20 optimal weight:    7.9990
   chunk 28 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    2.5444
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.051380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.040489 restraints weight = 45159.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.041502 restraints weight = 27257.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.042199 restraints weight = 19113.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.042706 restraints weight = 14681.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.042983 restraints weight = 12099.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10698  Z= 0.137
  Angle     :  0.587   9.080  14540  Z= 0.299
  Chirality :  0.042   0.158   1726
  Planarity :  0.004   0.027   1812
  Dihedral  :  4.329  22.579   1448
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.58 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  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: -0.21 (0.23), residues: 1346
  helix:  1.28 (0.18), residues: 828
  sheet:  2.76 (0.83), residues: 36
  loop : -3.10 (0.25), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 399 
 TYR   0.006   0.001   TYR B 118 
 PHE   0.017   0.001   PHE B 213 
 TRP   0.008   0.001   TRP B 472 
 HIS   0.017   0.003   HIS B  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (10698)
  covalent geometry    : angle       0.58709 (14540)
  hydrogen bonds       : bond        0.03838 (  602)
  hydrogen bonds       : angle       4.27588 ( 1788)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
REVERT: B  126 PHE cc_start: 0.8956 (m-80) cc_final: 0.8738 (m-80)
REVERT: B  225 MET cc_start: 0.9136 (mmp) cc_final: 0.8929 (mmp)
REVERT: B  357 MET cc_start: 0.8782 (tpt) cc_final: 0.8137 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0467
  time to fit residues: 3.0297
Evaluate side-chains
  29 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 122 optimal weight:    8.9990
   chunk 2 optimal weight:   10.0000
   chunk 118 optimal weight:    4.9990
   chunk 133 optimal weight:    3.9990
   chunk 102 optimal weight:   20.0000
   chunk 69 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9990
   chunk 112 optimal weight:    7.9990
   chunk 44 optimal weight:    9.9990
   chunk 124 optimal weight:    0.0060
   chunk 50 optimal weight:    0.8980
   overall best weight:    2.1802
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.051569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.040655 restraints weight = 45282.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.041582 restraints weight = 27416.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.042351 restraints weight = 19679.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.042840 restraints weight = 15026.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.043220 restraints weight = 12410.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10698  Z= 0.122
  Angle     :  0.560   6.537  14540  Z= 0.278
  Chirality :  0.042   0.155   1726
  Planarity :  0.003   0.022   1812
  Dihedral  :  4.089  17.116   1448
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.62 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  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: -0.68 (0.22), residues: 1346
  helix:  0.86 (0.18), residues: 834
  sheet:  2.66 (0.81), residues: 36
  loop : -3.24 (0.24), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 399 
 TYR   0.006   0.001   TYR A 546 
 PHE   0.009   0.001   PHE A 391 
 TRP   0.006   0.001   TRP B 472 
 HIS   0.010   0.002   HIS B  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (10698)
  covalent geometry    : angle       0.55985 (14540)
  hydrogen bonds       : bond        0.03497 (  602)
  hydrogen bonds       : angle       4.14820 ( 1788)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: B   93 LEU cc_start: 0.9318 (mm) cc_final: 0.8835 (pp)
REVERT: B  126 PHE cc_start: 0.8960 (m-80) cc_final: 0.8720 (m-80)
REVERT: B  225 MET cc_start: 0.9087 (mmp) cc_final: 0.8843 (mmp)
REVERT: B  575 MET cc_start: 0.9117 (mmp) cc_final: 0.8818 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 40
  average time/residue: 0.0495
  time to fit residues: 3.0927
Evaluate side-chains
  31 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 98 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 119 optimal weight:    0.8980
   chunk 66 optimal weight:    0.1980
   chunk 88 optimal weight:    6.9990
   chunk 34 optimal weight:   10.0000
   chunk 124 optimal weight:    6.9990
   chunk 42 optimal weight:    0.0870
   chunk 73 optimal weight:    8.9990
   overall best weight:    0.5758
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.052825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.041969 restraints weight = 45765.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.043006 restraints weight = 28497.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.043725 restraints weight = 20183.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.044169 restraints weight = 15599.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.044569 restraints weight = 13029.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  10698  Z= 0.105
  Angle     :  0.550   6.272  14540  Z= 0.269
  Chirality :  0.042   0.162   1726
  Planarity :  0.003   0.024   1812
  Dihedral  :  3.942  17.341   1448
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.02 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  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: -0.76 (0.22), residues: 1346
  helix:  0.74 (0.18), residues: 836
  sheet:  2.72 (0.79), residues: 36
  loop : -3.19 (0.24), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 716 
 TYR   0.006   0.001   TYR B 546 
 PHE   0.021   0.001   PHE B 213 
 TRP   0.004   0.000   TRP B 472 
 HIS   0.008   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 (10698)
  covalent geometry    : angle       0.54962 (14540)
  hydrogen bonds       : bond        0.03398 (  602)
  hydrogen bonds       : angle       4.01872 ( 1788)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 LEU cc_start: 0.9326 (mm) cc_final: 0.8754 (pp)
REVERT: B  126 PHE cc_start: 0.9016 (m-80) cc_final: 0.8766 (m-80)
REVERT: B  225 MET cc_start: 0.9107 (mmp) cc_final: 0.8807 (mmp)
REVERT: B  299 MET cc_start: 0.5890 (tpt) cc_final: 0.5533 (tpp)
REVERT: B  357 MET cc_start: 0.8788 (tpt) cc_final: 0.8248 (tpp)
REVERT: B  575 MET cc_start: 0.9173 (mmp) cc_final: 0.8925 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0493
  time to fit residues: 3.2558
Evaluate side-chains
  30 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 59 optimal weight:    0.0570
   chunk 78 optimal weight:    2.9990
   chunk 41 optimal weight:   10.0000
   chunk 127 optimal weight:    5.9990
   chunk 36 optimal weight:    8.9990
   chunk 3 optimal weight:   20.0000
   chunk 48 optimal weight:    0.0670
   chunk 54 optimal weight:    0.8980
   chunk 107 optimal weight:    6.9990
   chunk 34 optimal weight:   10.0000
   chunk 88 optimal weight:    0.2980
   overall best weight:    0.8638
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.052922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.041727 restraints weight = 44874.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.042805 restraints weight = 27124.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.043529 restraints weight = 18999.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.044107 restraints weight = 14661.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.044459 restraints weight = 12014.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  10698  Z= 0.104
  Angle     :  0.546   6.063  14540  Z= 0.266
  Chirality :  0.042   0.160   1726
  Planarity :  0.003   0.024   1812
  Dihedral  :  3.882  17.335   1448
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.32 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  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: -0.82 (0.22), residues: 1346
  helix:  0.69 (0.17), residues: 836
  sheet:  2.34 (0.78), residues: 36
  loop : -3.15 (0.24), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 716 
 TYR   0.010   0.001   TYR A 228 
 PHE   0.008   0.001   PHE B 391 
 TRP   0.005   0.001   TRP B 472 
 HIS   0.008   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (10698)
  covalent geometry    : angle       0.54583 (14540)
  hydrogen bonds       : bond        0.03170 (  602)
  hydrogen bonds       : angle       4.05516 ( 1788)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: B   93 LEU cc_start: 0.9340 (mm) cc_final: 0.8820 (pp)
REVERT: B  126 PHE cc_start: 0.8994 (m-80) cc_final: 0.8729 (m-80)
REVERT: B  299 MET cc_start: 0.5839 (tpt) cc_final: 0.5482 (tpp)
REVERT: B  357 MET cc_start: 0.8906 (tpt) cc_final: 0.8418 (tpp)
REVERT: B  453 MET cc_start: 0.6802 (mtt) cc_final: 0.5709 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0480
  time to fit residues: 3.0117
Evaluate side-chains
  28 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 124 optimal weight:   10.0000
   chunk 76 optimal weight:    0.9980
   chunk 132 optimal weight:   20.0000
   chunk 16 optimal weight:    6.9990
   chunk 2 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 125 optimal weight:    9.9990
   chunk 94 optimal weight:    8.9990
   chunk 34 optimal weight:    7.9990
   chunk 123 optimal weight:    9.9990
   chunk 110 optimal weight:    0.8980
   overall best weight:    2.0782
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.052333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.041245 restraints weight = 44654.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.042355 restraints weight = 27093.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.043104 restraints weight = 18867.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.043547 restraints weight = 14452.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.043964 restraints weight = 12039.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10698  Z= 0.114
  Angle     :  0.546   7.326  14540  Z= 0.268
  Chirality :  0.041   0.153   1726
  Planarity :  0.003   0.022   1812
  Dihedral  :  3.808  17.629   1448
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.47 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  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: -0.66 (0.22), residues: 1346
  helix:  0.86 (0.18), residues: 836
  sheet:  1.99 (0.79), residues: 36
  loop : -3.15 (0.24), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 399 
 TYR   0.008   0.001   TYR A 228 
 PHE   0.020   0.001   PHE B 213 
 TRP   0.003   0.001   TRP B 472 
 HIS   0.005   0.001   HIS B  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (10698)
  covalent geometry    : angle       0.54572 (14540)
  hydrogen bonds       : bond        0.03156 (  602)
  hydrogen bonds       : angle       3.99935 ( 1788)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: B   93 LEU cc_start: 0.9336 (mm) cc_final: 0.8803 (pp)
REVERT: B  126 PHE cc_start: 0.8996 (m-80) cc_final: 0.8727 (m-80)
REVERT: B  225 MET cc_start: 0.9029 (mmp) cc_final: 0.8815 (mmp)
REVERT: B  299 MET cc_start: 0.5849 (tpt) cc_final: 0.5475 (tpp)
REVERT: B  357 MET cc_start: 0.8936 (tpp) cc_final: 0.8367 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.0461
  time to fit residues: 2.8309
Evaluate side-chains
  28 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 128 optimal weight:    3.9990
   chunk 28 optimal weight:    8.9990
   chunk 47 optimal weight:    9.9990
   chunk 39 optimal weight:    0.0010
   chunk 87 optimal weight:    8.9990
   chunk 127 optimal weight:    0.9990
   chunk 123 optimal weight:    8.9990
   chunk 43 optimal weight:    0.0770
   chunk 105 optimal weight:    0.1980
   chunk 74 optimal weight:    5.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.0548
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.053002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.042073 restraints weight = 45454.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.043111 restraints weight = 27989.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.043874 restraints weight = 19764.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.044334 restraints weight = 15167.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.044732 restraints weight = 12611.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  10698  Z= 0.102
  Angle     :  0.570   9.557  14540  Z= 0.273
  Chirality :  0.042   0.158   1726
  Planarity :  0.003   0.025   1812
  Dihedral  :  3.807  17.335   1448
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.02 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  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: -0.68 (0.22), residues: 1346
  helix:  0.80 (0.18), residues: 836
  sheet:  1.99 (0.82), residues: 36
  loop : -3.07 (0.24), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 399 
 TYR   0.006   0.001   TYR A 228 
 PHE   0.011   0.001   PHE A 391 
 TRP   0.003   0.000   TRP B 472 
 HIS   0.009   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (10698)
  covalent geometry    : angle       0.57005 (14540)
  hydrogen bonds       : bond        0.03069 (  602)
  hydrogen bonds       : angle       3.99843 ( 1788)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
REVERT: B   93 LEU cc_start: 0.9326 (mm) cc_final: 0.8788 (pp)
REVERT: B  126 PHE cc_start: 0.8991 (m-80) cc_final: 0.8708 (m-80)
REVERT: B  225 MET cc_start: 0.9006 (mmp) cc_final: 0.8773 (mmp)
REVERT: B  299 MET cc_start: 0.5855 (tpt) cc_final: 0.5470 (tpp)
REVERT: B  357 MET cc_start: 0.8912 (tpp) cc_final: 0.8333 (tpp)
REVERT: B  453 MET cc_start: 0.6834 (mtt) cc_final: 0.6468 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.0462
  time to fit residues: 2.7110
Evaluate side-chains
  27 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 46 optimal weight:    7.9990
   chunk 132 optimal weight:    8.9990
   chunk 106 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0020
   chunk 58 optimal weight:    3.9990
   chunk 65 optimal weight:    8.9990
   chunk 72 optimal weight:    0.6980
   chunk 64 optimal weight:    6.9990
   chunk 75 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    1.2792
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.052887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.041813 restraints weight = 44775.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.042932 restraints weight = 27318.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.043651 restraints weight = 19036.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.044211 restraints weight = 14656.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.044535 restraints weight = 11988.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  10698  Z= 0.103
  Angle     :  0.561   7.264  14540  Z= 0.269
  Chirality :  0.042   0.156   1726
  Planarity :  0.003   0.025   1812
  Dihedral  :  3.776  17.549   1448
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.32 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  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: -0.59 (0.23), residues: 1346
  helix:  0.88 (0.18), residues: 836
  sheet:  1.90 (0.84), residues: 36
  loop : -3.05 (0.24), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 399 
 TYR   0.006   0.001   TYR A 228 
 PHE   0.020   0.001   PHE B 213 
 TRP   0.003   0.001   TRP A 472 
 HIS   0.004   0.001   HIS B  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (10698)
  covalent geometry    : angle       0.56135 (14540)
  hydrogen bonds       : bond        0.03053 (  602)
  hydrogen bonds       : angle       3.96226 ( 1788)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: B  126 PHE cc_start: 0.8997 (m-80) cc_final: 0.8703 (m-80)
REVERT: B  225 MET cc_start: 0.9002 (mmp) cc_final: 0.8692 (mmp)
REVERT: B  299 MET cc_start: 0.5848 (tpt) cc_final: 0.5456 (tpp)
REVERT: B  357 MET cc_start: 0.8910 (tpp) cc_final: 0.8406 (tpp)
REVERT: B  453 MET cc_start: 0.6866 (mtt) cc_final: 0.6509 (mtp)
REVERT: B  575 MET cc_start: 0.9187 (mmp) cc_final: 0.8929 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0489
  time to fit residues: 2.9585
Evaluate side-chains
  28 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 83 optimal weight:    7.9990
   chunk 23 optimal weight:    0.0030
   chunk 85 optimal weight:    0.0970
   chunk 9 optimal weight:    0.2980
   chunk 22 optimal weight:    0.2980
   chunk 50 optimal weight:    0.9980
   chunk 90 optimal weight:    0.0030
   chunk 53 optimal weight:    0.8980
   chunk 56 optimal weight:    9.9990
   chunk 18 optimal weight:    0.0970
   chunk 1 optimal weight:    4.9990
   overall best weight:    0.0996
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.054101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.043160 restraints weight = 45195.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.044249 restraints weight = 27828.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.045014 restraints weight = 19539.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.045550 restraints weight = 15076.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.045788 restraints weight = 12366.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.3064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  10698  Z= 0.103
  Angle     :  0.573   7.202  14540  Z= 0.273
  Chirality :  0.042   0.161   1726
  Planarity :  0.003   0.032   1812
  Dihedral  :  3.737  16.851   1448
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.73 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -0.72 (0.22), residues: 1346
  helix:  0.70 (0.17), residues: 840
  sheet:  1.98 (0.87), residues: 36
  loop : -2.96 (0.25), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 399 
 TYR   0.007   0.001   TYR A 546 
 PHE   0.008   0.001   PHE B 391 
 TRP   0.002   0.000   TRP B 462 
 HIS   0.013   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (10698)
  covalent geometry    : angle       0.57250 (14540)
  hydrogen bonds       : bond        0.03007 (  602)
  hydrogen bonds       : angle       4.00716 ( 1788)

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

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

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1346 Ramachandran restraints generated.
    673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: B  126 PHE cc_start: 0.9021 (m-80) cc_final: 0.8702 (m-80)
REVERT: B  225 MET cc_start: 0.8974 (mmp) cc_final: 0.8695 (mmp)
REVERT: B  299 MET cc_start: 0.5962 (tpt) cc_final: 0.5629 (tpp)
REVERT: B  357 MET cc_start: 0.8892 (tpp) cc_final: 0.8383 (tpp)
REVERT: B  453 MET cc_start: 0.6830 (mtt) cc_final: 0.6451 (mtp)
REVERT: B  575 MET cc_start: 0.9198 (mmp) cc_final: 0.8900 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0579
  time to fit residues: 3.7115
Evaluate side-chains
  30 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 102 optimal weight:   10.0000
   chunk 76 optimal weight:    0.0000
   chunk 39 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 77 optimal weight:   10.0000
   chunk 68 optimal weight:    5.9990
   chunk 133 optimal weight:    0.6980
   chunk 126 optimal weight:    0.0670
   overall best weight:    0.4922
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 220 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.054172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.043015 restraints weight = 45132.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.044134 restraints weight = 27619.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.044947 restraints weight = 19330.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.045475 restraints weight = 14710.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.045895 restraints weight = 12073.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.3161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  10698  Z= 0.102
  Angle     :  0.576   7.568  14540  Z= 0.279
  Chirality :  0.042   0.168   1726
  Planarity :  0.004   0.087   1812
  Dihedral  :  3.805  17.287   1448
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.58 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  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: -0.68 (0.22), residues: 1346
  helix:  0.75 (0.18), residues: 840
  sheet:  1.99 (0.90), residues: 36
  loop : -2.97 (0.25), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 502 
 TYR   0.007   0.001   TYR A 501 
 PHE   0.025   0.001   PHE B 213 
 TRP   0.003   0.000   TRP B 472 
 HIS   0.003   0.001   HIS A  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (10698)
  covalent geometry    : angle       0.57647 (14540)
  hydrogen bonds       : bond        0.03000 (  602)
  hydrogen bonds       : angle       3.91856 ( 1788)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1174.63 seconds
wall clock time: 21 minutes 20.74 seconds (1280.74 seconds total)