Starting phenix.real_space_refine
on Wed Mar  4 00:33:23 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xck_33123/03_2026/7xck_33123.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xck_33123/03_2026/7xck_33123.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xck_33123/03_2026/7xck_33123.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xck_33123/03_2026/7xck_33123.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xck_33123/03_2026/7xck_33123.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xck_33123/03_2026/7xck_33123.cif"
  }
  resolution = 2.5
  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=  -0.001 sd=   0.053
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4868 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    3473      2.51       5
     N     927      2.21       5
     O    1067      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5488
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1688
          Classifications: {'peptide': 223}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 210}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1615
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200}
    Chain: "M"
      Number of atoms: 2147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 269, 2147
          Classifications: {'peptide': 269}
          Link IDs: {'PTRANS': 16, 'TRANS': 252}
    Chain: "C"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.41, per 1000 atoms: 0.26
  Number of scatterers: 5488
  At special positions: 0
  Unit cell: (113.9, 61.64, 122.61, 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      21     16.00
     O    1067      8.00
     N     927      7.00
     C    3473      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 154 " - pdb=" SG  CYS A 210 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 134 " - pdb=" SG  CYS B 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 336 " - pdb=" SG  CYS M 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 379 " - pdb=" SG  CYS M 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS M 480 " - pdb=" SG  CYS M 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 538 " - pdb=" SG  CYS M 590 " 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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    BETA1-6
      " NAG C   1 " - " FUC C   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG C   1 " - " ASN M 343 "
  Time building additional restraints: 0.47
  Conformation dependent library (CDL) restraints added in 308.9 milliseconds
  

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1302

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 14 sheets defined
      9.7% alpha, 38.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 32
      removed outlier: 3.646A  pdb=" N   TYR A  32 " --> pdb=" O   PHE A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 65
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.942A  pdb=" N   THR A  91 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 32
      No H-bonds generated for 'chain 'B' and resid 30 through 32'
    Processing helix  chain 'B' and resid 80 through 84
      removed outlier: 4.031A  pdb=" N   PHE B  84 " --> pdb=" O   PRO B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 188
      removed outlier: 3.542A  pdb=" N   LYS B 188 " --> pdb=" O   ALA B 184 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 338 through 343
    Processing helix  chain 'M' and resid 365 through 369
    Processing helix  chain 'M' and resid 383 through 390
      removed outlier: 3.529A  pdb=" N   LEU M 387 " --> pdb=" O   PRO M 384 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ASN M 388 " --> pdb=" O   THR M 385 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   LEU M 390 " --> pdb=" O   LEU M 387 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 403 through 410
      removed outlier: 3.521A  pdb=" N   GLU M 406 " --> pdb=" O   ARG M 403 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   VAL M 407 " --> pdb=" O   GLY M 404 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ARG M 408 " --> pdb=" O   ASP M 405 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 416 through 422
    Processing helix  chain 'M' and resid 438 through 443
      removed outlier: 3.707A  pdb=" N   SER M 443 " --> pdb=" O   ASN M 439 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60
      removed outlier: 6.515A  pdb=" N   TRP A  36 " --> pdb=" O   MET A  48 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   TRP A  50 " --> pdb=" O   ILE A  34 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE A  34 " --> pdb=" O   TRP A  50 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ASN A 116 " --> pdb=" O   ARG A  98 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60
      removed outlier: 6.515A  pdb=" N   TRP A  36 " --> pdb=" O   MET A  48 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   TRP A  50 " --> pdb=" O   ILE A  34 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE A  34 " --> pdb=" O   TRP A  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 138
      removed outlier: 6.127A  pdb=" N   TYR A 190 " --> pdb=" O   ASP A 158 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 138
      removed outlier: 6.127A  pdb=" N   TYR A 190 " --> pdb=" O   ASP A 158 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 165 through 168
    Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.402A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   LEU B  34 " --> pdb=" O   TYR B  50 " (cutoff:3.500A)
      removed outlier: 4.706A  pdb=" N   TYR B  50 " --> pdb=" O   LEU B  34 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   TRP B  36 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.402A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118
      removed outlier: 3.957A  pdb=" N   VAL B 133 " --> pdb=" O   PHE B 118 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ASN B 138 " --> pdb=" O   TYR B 173 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   TYR B 173 " --> pdb=" O   ASN B 138 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 145 through 149
    Processing sheet with id=AB3, first strand: chain 'M' and resid 325 through 328
      removed outlier: 5.842A  pdb=" N   ASP M 574 " --> pdb=" O   ILE M 587 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   GLY M 566 " --> pdb=" O   ASP M 574 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'M' and resid 354 through 358
    Processing sheet with id=AB5, first strand: chain 'M' and resid 452 through 454

    209 hydrogen bonds defined for protein.
    513 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: 0.98

  Time building geometry restraints manager: 0.64 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 948
        1.32 -     1.45: 1605
        1.45 -     1.58: 3044
        1.58 -     1.71: 0
        1.71 -     1.84: 24
  Bond restraints: 5621
  Sorted by residual:
  bond pdb=" C   ALA M 344 "
       pdb=" N   THR M 345 "
    ideal  model  delta    sigma   weight residual
    1.335  1.278  0.057 1.25e-02 6.40e+03 2.05e+01
  bond pdb=" CA  ALA M 344 "
       pdb=" CB  ALA M 344 "
    ideal  model  delta    sigma   weight residual
    1.528  1.474  0.054 1.58e-02 4.01e+03 1.15e+01
  bond pdb=" C   ALA M 344 "
       pdb=" O   ALA M 344 "
    ideal  model  delta    sigma   weight residual
    1.235  1.201  0.034 1.20e-02 6.94e+03 8.18e+00
  bond pdb=" C   ASN M 343 "
       pdb=" O   ASN M 343 "
    ideal  model  delta    sigma   weight residual
    1.235  1.197  0.038 1.32e-02 5.74e+03 8.17e+00
  bond pdb=" CA  ALA M 344 "
       pdb=" C   ALA M 344 "
    ideal  model  delta    sigma   weight residual
    1.524  1.486  0.038 1.33e-02 5.65e+03 8.00e+00
  ... (remaining 5616 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.21: 7496
        2.21 -     4.43: 120
        4.43 -     6.64: 25
        6.64 -     8.85: 2
        8.85 -    11.07: 1
  Bond angle restraints: 7644
  Sorted by residual:
  angle pdb=" CA  ASN M 334 "
        pdb=" C   ASN M 334 "
        pdb=" O   ASN M 334 "
      ideal   model   delta    sigma   weight residual
     121.15  116.26    4.89 1.10e+00 8.26e-01 1.98e+01
  angle pdb=" C   VAL B 150 "
        pdb=" N   ASP B 151 "
        pdb=" CA  ASP B 151 "
      ideal   model   delta    sigma   weight residual
     121.54  129.19   -7.65 1.91e+00 2.74e-01 1.60e+01
  angle pdb=" C   ASN M 343 "
        pdb=" CA  ASN M 343 "
        pdb=" CB  ASN M 343 "
      ideal   model   delta    sigma   weight residual
     111.02  104.60    6.42 1.61e+00 3.86e-01 1.59e+01
  angle pdb=" C   PRO A 161 "
        pdb=" N   GLU A 162 "
        pdb=" CA  GLU A 162 "
      ideal   model   delta    sigma   weight residual
     120.26  125.14   -4.88 1.34e+00 5.57e-01 1.33e+01
  angle pdb=" C   SER B  95 "
        pdb=" CA  SER B  95 "
        pdb=" CB  SER B  95 "
      ideal   model   delta    sigma   weight residual
     115.89  111.20    4.69 1.32e+00 5.74e-01 1.26e+01
  ... (remaining 7639 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 3108
       17.59 -    35.17: 228
       35.17 -    52.76: 47
       52.76 -    70.34: 5
       70.34 -    87.93: 4
  Dihedral angle restraints: 3392
    sinusoidal: 1356
      harmonic: 2036
  Sorted by residual:
  dihedral pdb=" CB  CYS A 154 "
           pdb=" SG  CYS A 154 "
           pdb=" SG  CYS A 210 "
           pdb=" CB  CYS A 210 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.64  -69.64     1      1.00e+01 1.00e-02 6.26e+01
  dihedral pdb=" CB  CYS M 538 "
           pdb=" SG  CYS M 538 "
           pdb=" SG  CYS M 590 "
           pdb=" CB  CYS M 590 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -38.35  -47.65     1      1.00e+01 1.00e-02 3.13e+01
  dihedral pdb=" CB  CYS M 379 "
           pdb=" SG  CYS M 379 "
           pdb=" SG  CYS M 432 "
           pdb=" CB  CYS M 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -51.56  -34.44     1      1.00e+01 1.00e-02 1.68e+01
  ... (remaining 3389 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.142: 855
       0.142 -    0.284: 2
       0.284 -    0.425: 0
       0.425 -    0.567: 0
       0.567 -    0.709: 1
  Chirality restraints: 858
  Sorted by residual:
  chirality pdb=" C1  FUC C   3 "
            pdb=" O6  NAG C   1 "
            pdb=" C2  FUC C   3 "
            pdb=" O5  FUC C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.31   -0.09 2.00e-02 2.50e+03 2.19e+01
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN M 343 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.69   -0.71 2.00e-01 2.50e+01 1.26e+01
  chirality pdb=" CA  VAL A  37 "
            pdb=" N   VAL A  37 "
            pdb=" C   VAL A  37 "
            pdb=" CB  VAL A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.69e-01
  ... (remaining 855 not shown)

  Planarity restraints: 982
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "   -0.045 2.00e-02 2.50e+03   3.72e-02 1.73e+01
        pdb=" C7  NAG C   1 "    0.011 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "   -0.034 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "    0.060 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   2 "    0.041 2.00e-02 2.50e+03   3.36e-02 1.41e+01
        pdb=" C7  NAG C   2 "   -0.012 2.00e-02 2.50e+03
        pdb=" C8  NAG C   2 "    0.032 2.00e-02 2.50e+03
        pdb=" N2  NAG C   2 "   -0.052 2.00e-02 2.50e+03
        pdb=" O7  NAG C   2 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA M 520 "    0.043 5.00e-02 4.00e+02   6.51e-02 6.78e+00
        pdb=" N   PRO M 521 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO M 521 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO M 521 "    0.036 5.00e-02 4.00e+02
  ... (remaining 979 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 246
        2.72 -     3.27: 5007
        3.27 -     3.81: 8362
        3.81 -     4.36: 10652
        4.36 -     4.90: 18600
  Nonbonded interactions: 42867
  Sorted by model distance:
  nonbonded pdb=" OH  TYR M 369 "
            pdb=" O   PRO M 384 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" OG  SER B  64 "
            pdb=" OG1 THR B  75 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OG1 THR A 149 "
            pdb=" O   VAL A 198 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OE1 GLU B 105 "
            pdb=" OH  TYR B 173 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   ASP M 442 "
            pdb=" ND2 ASN M 448 "
     model   vdw
     2.307 3.120
  ... (remaining 42862 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 individual isotropic
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:             10.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.230
  Find NCS groups from input model:        0.020
  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:7.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
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      :  0.004   0.057   5632  Z= 0.203
  Angle     :  0.723  11.067   7669  Z= 0.392
  Chirality :  0.052   0.709    858
  Planarity :  0.006   0.065    981
  Dihedral  : 12.630  87.930   2066
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.60 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.89 (0.32), residues: 696
  helix: -3.99 (0.85), residues: 20
  sheet:  0.21 (0.33), residues: 271
  loop : -0.98 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG M 346 
 TYR   0.007   0.001   TYR A 159 
 PHE   0.012   0.001   PHE M 374 
 TRP   0.008   0.001   TRP M 436 
 HIS   0.004   0.001   HIS M 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 5621)
  covalent geometry    : angle       0.71268 ( 7644)
  SS BOND              : bond        0.00609 (    8)
  SS BOND              : angle       1.26856 (   16)
  hydrogen bonds       : bond        0.14772 (  181)
  hydrogen bonds       : angle       7.19690 (  513)
  link_BETA1-4         : bond        0.00179 (    1)
  link_BETA1-4         : angle       2.72332 (    3)
  link_BETA1-6         : bond        0.01807 (    1)
  link_BETA1-6         : angle       2.90036 (    3)
  link_NAG-ASN         : bond        0.02761 (    1)
  link_NAG-ASN         : angle       4.16457 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.7300
  time to fit residues: 52.3043
Evaluate side-chains
  57 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    0.0980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.4980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B 155 GLN
B 189 HIS
M 417 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.183099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.117815 restraints weight = 6216.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 2.54
r_work: 0.3273 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.0833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5632  Z= 0.126
  Angle     :  0.600   8.864   7669  Z= 0.309
  Chirality :  0.046   0.139    858
  Planarity :  0.005   0.060    981
  Dihedral  :  4.965  20.147    823
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  :  6.25 %
    Favored  : 91.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.89 (0.33), residues: 696
  helix: -4.44 (0.53), residues: 26
  sheet:  0.30 (0.33), residues: 271
  loop : -0.96 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  78 
 TYR   0.008   0.001   TYR A 159 
 PHE   0.013   0.001   PHE M 377 
 TRP   0.009   0.001   TRP A  47 
 HIS   0.004   0.001   HIS B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 5621)
  covalent geometry    : angle       0.59290 ( 7644)
  SS BOND              : bond        0.00603 (    8)
  SS BOND              : angle       1.41612 (   16)
  hydrogen bonds       : bond        0.03483 (  181)
  hydrogen bonds       : angle       5.72638 (  513)
  link_BETA1-4         : bond        0.00026 (    1)
  link_BETA1-4         : angle       2.36653 (    3)
  link_BETA1-6         : bond        0.00389 (    1)
  link_BETA1-6         : angle       1.81106 (    3)
  link_NAG-ASN         : bond        0.00476 (    1)
  link_NAG-ASN         : angle       2.15756 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7312 (mp10)
REVERT: A   82 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7642 (tp30)
REVERT: B  117 ILE cc_start: 0.6488 (tt) cc_final: 0.6050 (mm)
REVERT: M  357 ARG cc_start: 0.8722 (ttp-170) cc_final: 0.8308 (ttp80)
REVERT: M  405 ASP cc_start: 0.7838 (p0) cc_final: 0.7585 (p0)
REVERT: M  586 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7943 (m-30)
  outliers start: 15
  outliers final: 5
  residues processed: 71
  average time/residue: 0.6866
  time to fit residues: 50.6757
Evaluate side-chains
  64 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain M residue  332 ILE
Chi-restraints excluded: chain M residue  553 THR
Chi-restraints excluded: chain M residue  586 ASP
Chi-restraints excluded: chain M residue  588 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 37 optimal weight:   20.0000
   overall best weight:    2.3788

-------------------------------------------------------------------------------
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 = 0.4084 r_free = 0.4084 target = 0.179381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.113555 restraints weight = 6125.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 2.55
r_work: 0.3212 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050   5632  Z= 0.281
  Angle     :  0.719   8.650   7669  Z= 0.375
  Chirality :  0.050   0.178    858
  Planarity :  0.006   0.064    981
  Dihedral  :  5.509  20.295    823
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 12.01 %
    Favored  : 85.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.32), residues: 696
  helix: -4.40 (0.49), residues: 26
  sheet:  0.15 (0.32), residues: 278
  loop : -1.09 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  78 
 TYR   0.017   0.002   TYR B  37 
 PHE   0.026   0.002   PHE M 377 
 TRP   0.016   0.002   TRP A  50 
 HIS   0.007   0.002   HIS B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00684 ( 5621)
  covalent geometry    : angle       0.70903 ( 7644)
  SS BOND              : bond        0.01130 (    8)
  SS BOND              : angle       2.26946 (   16)
  hydrogen bonds       : bond        0.04549 (  181)
  hydrogen bonds       : angle       5.83180 (  513)
  link_BETA1-4         : bond        0.00020 (    1)
  link_BETA1-4         : angle       2.88337 (    3)
  link_BETA1-6         : bond        0.00288 (    1)
  link_BETA1-6         : angle       1.72935 (    3)
  link_NAG-ASN         : bond        0.00737 (    1)
  link_NAG-ASN         : angle       1.49199 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7426 (mp10)
REVERT: B  117 ILE cc_start: 0.6618 (tt) cc_final: 0.6232 (mm)
REVERT: M  357 ARG cc_start: 0.8764 (ttp-170) cc_final: 0.8380 (ttp-170)
REVERT: M  403 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.6868 (ttt-90)
REVERT: M  461 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7409 (pp)
REVERT: M  574 ASP cc_start: 0.7868 (p0) cc_final: 0.7345 (p0)
REVERT: M  586 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7946 (m-30)
  outliers start: 15
  outliers final: 7
  residues processed: 70
  average time/residue: 0.6394
  time to fit residues: 46.6864
Evaluate side-chains
  69 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain M residue  332 ILE
Chi-restraints excluded: chain M residue  333 THR
Chi-restraints excluded: chain M residue  403 ARG
Chi-restraints excluded: chain M residue  461 LEU
Chi-restraints excluded: chain M residue  470 THR
Chi-restraints excluded: chain M residue  553 THR
Chi-restraints excluded: chain M residue  586 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0370
   chunk 13 optimal weight:    9.9990
   chunk 49 optimal weight:    0.0070
   chunk 62 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 40 optimal weight:    9.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.4676

-------------------------------------------------------------------------------
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 = 0.4125 r_free = 0.4125 target = 0.183621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.119458 restraints weight = 6062.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 2.49
r_work: 0.3288 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.1214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5632  Z= 0.102
  Angle     :  0.554   7.846   7669  Z= 0.289
  Chirality :  0.044   0.136    858
  Planarity :  0.005   0.062    981
  Dihedral  :  4.761  21.543    823
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.97 %
    Favored  : 82.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.78 (0.32), residues: 696
  helix: -4.20 (0.56), residues: 26
  sheet:  0.45 (0.33), residues: 268
  loop : -0.95 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  78 
 TYR   0.009   0.001   TYR B 140 
 PHE   0.011   0.001   PHE M 374 
 TRP   0.010   0.001   TRP A  47 
 HIS   0.003   0.001   HIS B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 5621)
  covalent geometry    : angle       0.54966 ( 7644)
  SS BOND              : bond        0.00470 (    8)
  SS BOND              : angle       1.04997 (   16)
  hydrogen bonds       : bond        0.03060 (  181)
  hydrogen bonds       : angle       5.37761 (  513)
  link_BETA1-4         : bond        0.00138 (    1)
  link_BETA1-4         : angle       2.17716 (    3)
  link_BETA1-6         : bond        0.00074 (    1)
  link_BETA1-6         : angle       1.41067 (    3)
  link_NAG-ASN         : bond        0.00425 (    1)
  link_NAG-ASN         : angle       1.79850 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7429 (mp10)
REVERT: A   89 ASP cc_start: 0.8192 (m-30) cc_final: 0.7325 (t0)
REVERT: B  117 ILE cc_start: 0.6563 (tt) cc_final: 0.6188 (mm)
REVERT: B  166 GLN cc_start: 0.6875 (tt0) cc_final: 0.6491 (tt0)
REVERT: M  357 ARG cc_start: 0.8801 (ttp-170) cc_final: 0.8264 (ttp80)
REVERT: M  405 ASP cc_start: 0.7830 (p0) cc_final: 0.7603 (p0)
REVERT: M  461 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7097 (pp)
REVERT: M  574 ASP cc_start: 0.7952 (p0) cc_final: 0.7417 (p0)
REVERT: M  586 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7972 (m-30)
  outliers start: 14
  outliers final: 5
  residues processed: 69
  average time/residue: 0.6331
  time to fit residues: 45.5933
Evaluate side-chains
  67 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain M residue  332 ILE
Chi-restraints excluded: chain M residue  333 THR
Chi-restraints excluded: chain M residue  461 LEU
Chi-restraints excluded: chain M residue  586 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0670
   chunk 44 optimal weight:    0.0980
   chunk 40 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 20 optimal weight:    9.9990
   chunk 56 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0970
   chunk 23 optimal weight:    4.9990
   overall best weight:    1.0520

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.181868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.117000 restraints weight = 6223.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 2.53
r_work: 0.3255 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.1263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5632  Z= 0.144
  Angle     :  0.598   8.446   7669  Z= 0.307
  Chirality :  0.046   0.144    858
  Planarity :  0.005   0.058    981
  Dihedral  :  4.820  21.212    823
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 14.97 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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 (0.32), residues: 696
  helix: -4.18 (0.57), residues: 26
  sheet:  0.55 (0.33), residues: 262
  loop : -0.98 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  78 
 TYR   0.009   0.001   TYR B  37 
 PHE   0.015   0.001   PHE M 377 
 TRP   0.011   0.001   TRP A  47 
 HIS   0.005   0.001   HIS B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 5621)
  covalent geometry    : angle       0.59233 ( 7644)
  SS BOND              : bond        0.00776 (    8)
  SS BOND              : angle       1.44811 (   16)
  hydrogen bonds       : bond        0.03415 (  181)
  hydrogen bonds       : angle       5.42424 (  513)
  link_BETA1-4         : bond        0.00166 (    1)
  link_BETA1-4         : angle       2.31362 (    3)
  link_BETA1-6         : bond        0.00127 (    1)
  link_BETA1-6         : angle       1.48977 (    3)
  link_NAG-ASN         : bond        0.00511 (    1)
  link_NAG-ASN         : angle       1.53836 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A   43 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7484 (mp10)
REVERT: A   89 ASP cc_start: 0.8168 (m-30) cc_final: 0.7314 (t0)
REVERT: B  117 ILE cc_start: 0.6497 (tt) cc_final: 0.6136 (mm)
REVERT: B  166 GLN cc_start: 0.6865 (tt0) cc_final: 0.6438 (tt0)
REVERT: M  357 ARG cc_start: 0.8802 (ttp-170) cc_final: 0.8284 (ttp-170)
REVERT: M  403 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.6737 (ttt-90)
REVERT: M  461 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7118 (pp)
REVERT: M  465 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7883 (tt0)
REVERT: M  574 ASP cc_start: 0.7907 (p0) cc_final: 0.7360 (p0)
REVERT: M  586 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7967 (m-30)
  outliers start: 17
  outliers final: 7
  residues processed: 70
  average time/residue: 0.6018
  time to fit residues: 43.9229
Evaluate side-chains
  69 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain M residue  332 ILE
Chi-restraints excluded: chain M residue  333 THR
Chi-restraints excluded: chain M residue  403 ARG
Chi-restraints excluded: chain M residue  461 LEU
Chi-restraints excluded: chain M residue  465 GLU
Chi-restraints excluded: chain M residue  572 THR
Chi-restraints excluded: chain M residue  586 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 19 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 34 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
M 505 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.183616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.122003 restraints weight = 6195.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 2.38
r_work: 0.3328 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   5632  Z= 0.212
  Angle     :  0.669  10.512   7669  Z= 0.346
  Chirality :  0.049   0.287    858
  Planarity :  0.006   0.062    981
  Dihedral  :  5.121  20.594    823
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 15.46 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.85 (0.32), residues: 696
  helix: -4.26 (0.53), residues: 26
  sheet:  0.47 (0.33), residues: 268
  loop : -1.05 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  24 
 TYR   0.014   0.002   TYR M 380 
 PHE   0.021   0.002   PHE M 377 
 TRP   0.014   0.001   TRP A  50 
 HIS   0.006   0.001   HIS B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 5621)
  covalent geometry    : angle       0.65975 ( 7644)
  SS BOND              : bond        0.01289 (    8)
  SS BOND              : angle       2.08489 (   16)
  hydrogen bonds       : bond        0.03968 (  181)
  hydrogen bonds       : angle       5.50968 (  513)
  link_BETA1-4         : bond        0.00204 (    1)
  link_BETA1-4         : angle       2.53885 (    3)
  link_BETA1-6         : bond        0.00185 (    1)
  link_BETA1-6         : angle       1.59091 (    3)
  link_NAG-ASN         : bond        0.00595 (    1)
  link_NAG-ASN         : angle       1.37851 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.8527 (mm-40) cc_final: 0.7987 (mp10)
REVERT: B   24 ARG cc_start: 0.7625 (tpp-160) cc_final: 0.7423 (tpp-160)
REVERT: B  117 ILE cc_start: 0.6811 (tt) cc_final: 0.6481 (mm)
REVERT: M  403 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7360 (ttt-90)
REVERT: M  461 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7594 (pp)
REVERT: M  465 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8056 (tt0)
REVERT: M  574 ASP cc_start: 0.8187 (p0) cc_final: 0.7707 (p0)
REVERT: M  586 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8198 (m-30)
  outliers start: 17
  outliers final: 9
  residues processed: 68
  average time/residue: 0.5538
  time to fit residues: 39.3781
Evaluate side-chains
  68 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain M residue  332 ILE
Chi-restraints excluded: chain M residue  333 THR
Chi-restraints excluded: chain M residue  403 ARG
Chi-restraints excluded: chain M residue  461 LEU
Chi-restraints excluded: chain M residue  465 GLU
Chi-restraints excluded: chain M residue  572 THR
Chi-restraints excluded: chain M residue  581 THR
Chi-restraints excluded: chain M residue  586 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 55 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.4184 r_free = 0.4184 target = 0.184586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.121416 restraints weight = 6194.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 2.46
r_work: 0.3346 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5632  Z= 0.150
  Angle     :  0.647  11.721   7669  Z= 0.331
  Chirality :  0.047   0.332    858
  Planarity :  0.005   0.062    981
  Dihedral  :  4.939  20.620    823
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 16.28 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.77 (0.32), residues: 696
  helix: -4.20 (0.57), residues: 26
  sheet:  0.60 (0.33), residues: 262
  loop : -1.03 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG M 357 
 TYR   0.011   0.001   TYR M 380 
 PHE   0.017   0.001   PHE M 377 
 TRP   0.012   0.001   TRP A  47 
 HIS   0.005   0.001   HIS B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 5621)
  covalent geometry    : angle       0.63882 ( 7644)
  SS BOND              : bond        0.01187 (    8)
  SS BOND              : angle       1.97706 (   16)
  hydrogen bonds       : bond        0.03480 (  181)
  hydrogen bonds       : angle       5.37018 (  513)
  link_BETA1-4         : bond        0.00188 (    1)
  link_BETA1-4         : angle       2.28160 (    3)
  link_BETA1-6         : bond        0.00109 (    1)
  link_BETA1-6         : angle       1.50876 (    3)
  link_NAG-ASN         : bond        0.00488 (    1)
  link_NAG-ASN         : angle       1.51323 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7938 (mp10)
REVERT: B  117 ILE cc_start: 0.6776 (tt) cc_final: 0.6402 (mm)
REVERT: B  166 GLN cc_start: 0.7214 (tt0) cc_final: 0.6789 (tt0)
REVERT: M  357 ARG cc_start: 0.8907 (ttp-170) cc_final: 0.8498 (ttp80)
REVERT: M  403 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.6895 (ttt-90)
REVERT: M  461 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7471 (pp)
REVERT: M  465 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8030 (tt0)
REVERT: M  574 ASP cc_start: 0.8175 (p0) cc_final: 0.7687 (p0)
REVERT: M  586 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8199 (m-30)
  outliers start: 17
  outliers final: 9
  residues processed: 67
  average time/residue: 0.5696
  time to fit residues: 39.8444
Evaluate side-chains
  70 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain M residue  332 ILE
Chi-restraints excluded: chain M residue  333 THR
Chi-restraints excluded: chain M residue  345 THR
Chi-restraints excluded: chain M residue  403 ARG
Chi-restraints excluded: chain M residue  461 LEU
Chi-restraints excluded: chain M residue  465 GLU
Chi-restraints excluded: chain M residue  572 THR
Chi-restraints excluded: chain M residue  581 THR
Chi-restraints excluded: chain M residue  586 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 3 optimal weight:    0.4980
   chunk 38 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 20 optimal weight:   20.0000
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.4186 r_free = 0.4186 target = 0.184789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.121915 restraints weight = 6079.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 2.44
r_work: 0.3352 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.1459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   5632  Z= 0.141
  Angle     :  0.632  12.023   7669  Z= 0.322
  Chirality :  0.047   0.284    858
  Planarity :  0.005   0.061    981
  Dihedral  :  4.814  20.569    823
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.78 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.67 (0.32), residues: 696
  helix: -4.18 (0.60), residues: 26
  sheet:  0.67 (0.33), residues: 262
  loop : -0.97 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG M 357 
 TYR   0.008   0.001   TYR B  37 
 PHE   0.015   0.001   PHE M 377 
 TRP   0.011   0.001   TRP A  47 
 HIS   0.005   0.001   HIS B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 5621)
  covalent geometry    : angle       0.62410 ( 7644)
  SS BOND              : bond        0.01077 (    8)
  SS BOND              : angle       1.83281 (   16)
  hydrogen bonds       : bond        0.03373 (  181)
  hydrogen bonds       : angle       5.29021 (  513)
  link_BETA1-4         : bond        0.00176 (    1)
  link_BETA1-4         : angle       2.20812 (    3)
  link_BETA1-6         : bond        0.00081 (    1)
  link_BETA1-6         : angle       1.47970 (    3)
  link_NAG-ASN         : bond        0.00490 (    1)
  link_NAG-ASN         : angle       1.48829 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 57
  time to evaluate  : 0.205 
Fit side-chains
REVERT: A   43 GLN cc_start: 0.8439 (mm-40) cc_final: 0.7904 (mp10)
REVERT: B   78 ARG cc_start: 0.7318 (ttp80) cc_final: 0.7093 (ttp80)
REVERT: B  166 GLN cc_start: 0.7265 (tt0) cc_final: 0.6906 (tt0)
REVERT: M  403 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.6989 (ttt-90)
REVERT: M  461 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7329 (pp)
REVERT: M  465 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8018 (tt0)
REVERT: M  574 ASP cc_start: 0.8182 (p0) cc_final: 0.7701 (p0)
REVERT: M  586 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8172 (m-30)
  outliers start: 19
  outliers final: 12
  residues processed: 71
  average time/residue: 0.5961
  time to fit residues: 44.1386
Evaluate side-chains
  71 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain M residue  332 ILE
Chi-restraints excluded: chain M residue  333 THR
Chi-restraints excluded: chain M residue  345 THR
Chi-restraints excluded: chain M residue  403 ARG
Chi-restraints excluded: chain M residue  461 LEU
Chi-restraints excluded: chain M residue  465 GLU
Chi-restraints excluded: chain M residue  572 THR
Chi-restraints excluded: chain M residue  581 THR
Chi-restraints excluded: chain M residue  586 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 59 optimal weight:    7.9990
   chunk 46 optimal weight:    1.9990
   chunk 20 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    1.5388

-------------------------------------------------------------------------------
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 = 0.4176 r_free = 0.4176 target = 0.183631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.120394 restraints weight = 6087.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 2.44
r_work: 0.3329 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.1520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5632  Z= 0.192
  Angle     :  0.694  13.426   7669  Z= 0.353
  Chirality :  0.049   0.305    858
  Planarity :  0.006   0.062    981
  Dihedral  :  5.117  24.478    823
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 17.11 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.80 (0.32), residues: 696
  helix: -4.26 (0.55), residues: 26
  sheet:  0.62 (0.34), residues: 261
  loop : -1.07 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG M 357 
 TYR   0.012   0.002   TYR M 380 
 PHE   0.022   0.002   PHE M 377 
 TRP   0.013   0.001   TRP A  50 
 HIS   0.006   0.001   HIS B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 5621)
  covalent geometry    : angle       0.68628 ( 7644)
  SS BOND              : bond        0.01249 (    8)
  SS BOND              : angle       1.90331 (   16)
  hydrogen bonds       : bond        0.03752 (  181)
  hydrogen bonds       : angle       5.43708 (  513)
  link_BETA1-4         : bond        0.00186 (    1)
  link_BETA1-4         : angle       2.44743 (    3)
  link_BETA1-6         : bond        0.00156 (    1)
  link_BETA1-6         : angle       1.54714 (    3)
  link_NAG-ASN         : bond        0.00563 (    1)
  link_NAG-ASN         : angle       1.38961 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A   43 GLN cc_start: 0.8457 (mm-40) cc_final: 0.7923 (mp10)
REVERT: M  357 ARG cc_start: 0.8920 (ttp-170) cc_final: 0.8531 (ttp80)
REVERT: M  403 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7025 (ttt-90)
REVERT: M  461 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7549 (pp)
REVERT: M  465 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8064 (tt0)
REVERT: M  574 ASP cc_start: 0.8182 (p0) cc_final: 0.7672 (p0)
REVERT: M  586 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8137 (m-30)
  outliers start: 18
  outliers final: 12
  residues processed: 70
  average time/residue: 0.5593
  time to fit residues: 40.8980
Evaluate side-chains
  71 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain M residue  332 ILE
Chi-restraints excluded: chain M residue  333 THR
Chi-restraints excluded: chain M residue  345 THR
Chi-restraints excluded: chain M residue  403 ARG
Chi-restraints excluded: chain M residue  461 LEU
Chi-restraints excluded: chain M residue  465 GLU
Chi-restraints excluded: chain M residue  553 THR
Chi-restraints excluded: chain M residue  572 THR
Chi-restraints excluded: chain M residue  581 THR
Chi-restraints excluded: chain M residue  586 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 49 optimal weight:   30.0000
   overall best weight:    1.5588

-------------------------------------------------------------------------------
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 = 0.4175 r_free = 0.4175 target = 0.183534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.120280 restraints weight = 6080.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.44
r_work: 0.3330 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.1565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   5632  Z= 0.194
  Angle     :  0.708  13.310   7669  Z= 0.358
  Chirality :  0.049   0.292    858
  Planarity :  0.006   0.063    981
  Dihedral  :  5.176  24.690    823
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 17.43 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.81 (0.32), residues: 696
  helix: -4.30 (0.53), residues: 26
  sheet:  0.48 (0.33), residues: 271
  loop : -1.02 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  78 
 TYR   0.012   0.002   TYR B  37 
 PHE   0.020   0.002   PHE M 377 
 TRP   0.013   0.001   TRP A  50 
 HIS   0.006   0.001   HIS B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 5621)
  covalent geometry    : angle       0.70041 ( 7644)
  SS BOND              : bond        0.01251 (    8)
  SS BOND              : angle       1.93175 (   16)
  hydrogen bonds       : bond        0.03752 (  181)
  hydrogen bonds       : angle       5.47533 (  513)
  link_BETA1-4         : bond        0.00134 (    1)
  link_BETA1-4         : angle       2.45892 (    3)
  link_BETA1-6         : bond        0.00234 (    1)
  link_BETA1-6         : angle       1.54863 (    3)
  link_NAG-ASN         : bond        0.00550 (    1)
  link_NAG-ASN         : angle       1.40206 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A   43 GLN cc_start: 0.8462 (mm-40) cc_final: 0.7928 (mp10)
REVERT: B  166 GLN cc_start: 0.7290 (tt0) cc_final: 0.6908 (tt0)
REVERT: M  357 ARG cc_start: 0.8910 (ttp-170) cc_final: 0.8543 (ttp80)
REVERT: M  403 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7035 (ttt-90)
REVERT: M  461 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7553 (pp)
REVERT: M  465 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8067 (tt0)
REVERT: M  574 ASP cc_start: 0.8182 (p0) cc_final: 0.7682 (p0)
REVERT: M  586 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8151 (m-30)
  outliers start: 17
  outliers final: 12
  residues processed: 71
  average time/residue: 0.5921
  time to fit residues: 43.8587
Evaluate side-chains
  72 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain M residue  332 ILE
Chi-restraints excluded: chain M residue  333 THR
Chi-restraints excluded: chain M residue  345 THR
Chi-restraints excluded: chain M residue  403 ARG
Chi-restraints excluded: chain M residue  461 LEU
Chi-restraints excluded: chain M residue  465 GLU
Chi-restraints excluded: chain M residue  553 THR
Chi-restraints excluded: chain M residue  572 THR
Chi-restraints excluded: chain M residue  581 THR
Chi-restraints excluded: chain M residue  586 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 20 optimal weight:   20.0000
   chunk 46 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 65 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
B 137 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.182595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.119176 restraints weight = 6132.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 2.44
r_work: 0.3318 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.1632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   5632  Z= 0.237
  Angle     :  0.750  13.403   7669  Z= 0.381
  Chirality :  0.050   0.299    858
  Planarity :  0.007   0.079    981
  Dihedral  :  5.414  25.439    823
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.27 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.92 (0.32), residues: 696
  helix: -4.37 (0.50), residues: 26
  sheet:  0.35 (0.32), residues: 277
  loop : -1.06 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  78 
 TYR   0.014   0.002   TYR B  37 
 PHE   0.024   0.002   PHE M 377 
 TRP   0.015   0.002   TRP A  50 
 HIS   0.006   0.001   HIS B  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00575 ( 5621)
  covalent geometry    : angle       0.74198 ( 7644)
  SS BOND              : bond        0.01368 (    8)
  SS BOND              : angle       2.10824 (   16)
  hydrogen bonds       : bond        0.04090 (  181)
  hydrogen bonds       : angle       5.57432 (  513)
  link_BETA1-4         : bond        0.00163 (    1)
  link_BETA1-4         : angle       2.67055 (    3)
  link_BETA1-6         : bond        0.00239 (    1)
  link_BETA1-6         : angle       1.60000 (    3)
  link_NAG-ASN         : bond        0.00613 (    1)
  link_NAG-ASN         : angle       1.33655 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3306.36 seconds
wall clock time: 56 minutes 44.00 seconds (3404.00 seconds total)