Starting phenix.real_space_refine
on Wed Jul  1 23:12:51 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7wn1_32619/07_2026/7wn1_32619.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wn1_32619/07_2026/7wn1_32619.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7wn1_32619/07_2026/7wn1_32619.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7wn1_32619/07_2026/7wn1_32619.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wn1_32619/07_2026/7wn1_32619.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wn1_32619/07_2026/7wn1_32619.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wn1_32619/07_2026/7wn1_32619.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wn1_32619/07_2026/7wn1_32619.map"
  }
  resolution = 3.11
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
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=   0.033
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      26      5.16       5
     C    2572      2.51       5
     N     616      2.21       5
     O     687      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3901
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2953
          Classifications: {'peptide': 371}
          Link IDs: {'PTRANS': 11, 'TRANS': 359}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 929
          Classifications: {'peptide': 122}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "A"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 19
          Unusual residues: {'NOS%rna2p': 1}
          Classifications: {'undetermined': 1}
          Modifications used: {'rna2p': 1}
  Time building chain proxies: 1.03, per 1000 atoms: 0.26
  Number of scatterers: 3901
  At special positions: 0
  Unit cell: (110.39, 60.59, 64.74, 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      26     16.00
     O     687      8.00
     N     616      7.00
     C    2572      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " 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
  Time building additional restraints: 0.38
  Conformation dependent library (CDL) restraints added in 174.6 milliseconds
  

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  914

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 3 sheets defined
      64.3% alpha, 13.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 31 through 59
      removed outlier: 4.331A  pdb=" N   VAL A  52 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   TRP A  53 " --> pdb=" O   SER A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 83
      removed outlier: 3.547A  pdb=" N   ASN A  66 " --> pdb=" O   ASN A  62 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   PHE A  82 " --> pdb=" O   ILE A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 88
      No H-bonds generated for 'chain 'A' and resid 86 through 88'
    Processing helix  chain 'A' and resid 89 through 111
    Processing helix  chain 'A' and resid 112 through 144
    Processing helix  chain 'A' and resid 149 through 175
      removed outlier: 3.802A  pdb=" N   GLN A 173 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   PHE A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 210
    Processing helix  chain 'A' and resid 231 through 239
    Processing helix  chain 'A' and resid 239 through 257
      removed outlier: 3.734A  pdb=" N   ILE A 243 " --> pdb=" O   SER A 239 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ASN A 250 " --> pdb=" O   MET A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 270
      removed outlier: 3.674A  pdb=" N   GLN A 266 " --> pdb=" O   HIS A 262 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLU A 267 " --> pdb=" O   LYS A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 290
      removed outlier: 3.759A  pdb=" N   THR A 277 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ILE A 278 " --> pdb=" O   TYR A 274 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   PHE A 283 " --> pdb=" O   ILE A 279 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   PHE A 288 " --> pdb=" O   GLN A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 296
      removed outlier: 3.967A  pdb=" N   ASN A 295 " --> pdb=" O   ARG A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 319
    Processing helix  chain 'A' and resid 321 through 332
      removed outlier: 3.538A  pdb=" N   TRP A 325 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA A 330 " --> pdb=" O   PHE A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 369
      removed outlier: 3.804A  pdb=" N   LEU A 350 " --> pdb=" O   CYS A 346 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   THR A 359 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      Proline residue:  A 361  - end of helix
      removed outlier: 5.181A  pdb=" N   VAL A 366 " --> pdb=" O   PHE A 362 " (cutoff:3.500A)
      removed outlier: 5.787A  pdb=" N   LYS A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLU A 368 " --> pdb=" O   VAL A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 400
      removed outlier: 3.655A  pdb=" N   ILE A 378 " --> pdb=" O   LYS A 374 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   THR A 400 " --> pdb=" O   GLY A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 405
    Processing helix  chain 'C' and resid 86 through 90
    Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 7
    Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.193A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 119 " (cutoff:3.500A)
      removed outlier: 5.513A  pdb=" N   ARG C  38 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   LEU C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.193A  pdb=" N   GLY C  10 " --> pdb=" O   THR C 119 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLN C 109 " --> pdb=" O   THR C  99 " (cutoff:3.500A)

    260 hydrogen bonds defined for protein.
    750 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.37

  Time building geometry restraints manager: 0.49 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 823
        1.33 -     1.45: 929
        1.45 -     1.57: 2205
        1.57 -     1.69: 2
        1.69 -     1.81: 39
  Bond restraints: 3998
  Sorted by residual:
  bond pdb=" C1' NOS A 501 "
       pdb=" O4' NOS A 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.600 -0.203 2.00e-02 2.50e+03 1.03e+02
  bond pdb=" C1' NOS A 501 "
       pdb=" C2' NOS A 501 "
    ideal  model  delta    sigma   weight residual
    1.528  1.346  0.182 2.00e-02 2.50e+03 8.30e+01
  bond pdb=" C2  NOS A 501 "
       pdb=" N3  NOS A 501 "
    ideal  model  delta    sigma   weight residual
    1.293  1.444 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" C4  NOS A 501 "
       pdb=" N3  NOS A 501 "
    ideal  model  delta    sigma   weight residual
    1.347  1.497 -0.150 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" C4' NOS A 501 "
       pdb=" O4' NOS A 501 "
    ideal  model  delta    sigma   weight residual
    1.432  1.309  0.123 2.00e-02 2.50e+03 3.77e+01
  ... (remaining 3993 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 5331
        2.00 -     4.00: 75
        4.00 -     6.00: 17
        6.00 -     8.00: 4
        8.00 -    10.00: 2
  Bond angle restraints: 5429
  Sorted by residual:
  angle pdb=" C5  NOS A 501 "
        pdb=" C6  NOS A 501 "
        pdb=" O6  NOS A 501 "
      ideal   model   delta    sigma   weight residual
     128.65  118.65   10.00 3.00e+00 1.11e-01 1.11e+01
  angle pdb=" N   SER A 308 "
        pdb=" CA  SER A 308 "
        pdb=" C   SER A 308 "
      ideal   model   delta    sigma   weight residual
     107.88  112.42   -4.54 1.41e+00 5.03e-01 1.04e+01
  angle pdb=" C3' NOS A 501 "
        pdb=" C2' NOS A 501 "
        pdb=" O2' NOS A 501 "
      ideal   model   delta    sigma   weight residual
     116.89  107.68    9.21 3.00e+00 1.11e-01 9.42e+00
  angle pdb=" C   TYR C  37 "
        pdb=" N   ARG C  38 "
        pdb=" CA  ARG C  38 "
      ideal   model   delta    sigma   weight residual
     122.65  118.88    3.77 1.49e+00 4.50e-01 6.40e+00
  angle pdb=" C2  NOS A 501 "
        pdb=" N3  NOS A 501 "
        pdb=" C4  NOS A 501 "
      ideal   model   delta    sigma   weight residual
     112.58  119.70   -7.12 3.00e+00 1.11e-01 5.63e+00
  ... (remaining 5424 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.24: 2042
       15.24 -    30.48: 191
       30.48 -    45.71: 52
       45.71 -    60.95: 13
       60.95 -    76.19: 3
  Dihedral angle restraints: 2301
    sinusoidal: 877
      harmonic: 1424
  Sorted by residual:
  dihedral pdb=" CA  LEU A 256 "
           pdb=" C   LEU A 256 "
           pdb=" N   PHE A 257 "
           pdb=" CA  PHE A 257 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.88  -18.12     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  MET A 145 "
           pdb=" C   MET A 145 "
           pdb=" N   GLU A 146 "
           pdb=" CA  GLU A 146 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.85   17.15     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CA  VAL A 332 "
           pdb=" C   VAL A 332 "
           pdb=" N   ASP A 333 "
           pdb=" CA  ASP A 333 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.41  -15.59     0      5.00e+00 4.00e-02 9.72e+00
  ... (remaining 2298 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 372
       0.031 -    0.061: 174
       0.061 -    0.092: 56
       0.092 -    0.122: 20
       0.122 -    0.153: 8
  Chirality restraints: 630
  Sorted by residual:
  chirality pdb=" CB  ILE A 193 "
            pdb=" CA  ILE A 193 "
            pdb=" CG1 ILE A 193 "
            pdb=" CG2 ILE A 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.82e-01
  chirality pdb=" C1' NOS A 501 "
            pdb=" C2' NOS A 501 "
            pdb=" N9  NOS A 501 "
            pdb=" O4' NOS A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.36    2.50   -0.14 2.00e-01 2.50e+01 5.12e-01
  chirality pdb=" CA  ASP A 147 "
            pdb=" N   ASP A 147 "
            pdb=" C   ASP A 147 "
            pdb=" CB  ASP A 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.10e-01
  ... (remaining 627 not shown)

  Planarity restraints: 665
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 257 "   -0.023 5.00e-02 4.00e+02   3.53e-02 1.99e+00
        pdb=" N   PRO A 258 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 258 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 258 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 334 "   -0.021 5.00e-02 4.00e+02   3.24e-02 1.68e+00
        pdb=" N   PRO A 335 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 335 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 335 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 412 "   -0.020 5.00e-02 4.00e+02   3.08e-02 1.51e+00
        pdb=" N   PRO A 413 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 413 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 413 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 662 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 835
        2.78 -     3.31: 3841
        3.31 -     3.84: 6568
        3.84 -     4.37: 7875
        4.37 -     4.90: 13686
  Nonbonded interactions: 32805
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  65 "
            pdb=" OD1 ASP A 117 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OG1 THR A  41 "
            pdb=" OD1 ASN A 209 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   CYS A 395 "
            pdb=" OG1 THR A 399 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O   LEU A 256 "
            pdb=" N   GLY A 261 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" NE2 GLN C  81 "
            pdb=" OD1 ASN C  83 "
     model   vdw
     2.320 3.120
  ... (remaining 32800 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:             1.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     4.830
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8690
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      :  0.007   0.203   3999  Z= 0.360
  Angle     :  0.651  10.003   5431  Z= 0.333
  Chirality :  0.042   0.153    630
  Planarity :  0.004   0.035    665
  Dihedral  : 13.490  76.187   1384
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  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:  1.00 (0.38), residues: 487
  helix:  1.09 (0.30), residues: 285
  sheet:  0.84 (0.64), residues: 58
  loop : -0.10 (0.58), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 319 
 TYR   0.018   0.001   TYR C 102 
 PHE   0.016   0.001   PHE C  27 
 TRP   0.009   0.001   TRP A 251 
 HIS   0.004   0.001   HIS A 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00727 /  0.36 ( 3998)
  covalent geometry    : angle       0.65079 /  0.33 ( 5429)
  SS BOND              : bond        0.00151 /  0.08 (    1)
  SS BOND              : angle       0.17564 /  0.09 (    2)
  hydrogen bonds       : bond        0.18087 / 12.48 (  256)
  hydrogen bonds       : angle       6.16735 /  4.57 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A  175 VAL cc_start: 0.8097 (t) cc_final: 0.7828 (m)
REVERT: A  303 LYS cc_start: 0.8628 (tppt) cc_final: 0.8418 (tppt)
REVERT: A  407 ASN cc_start: 0.8197 (t0) cc_final: 0.7963 (t0)
REVERT: C   94 TYR cc_start: 0.8213 (m-10) cc_final: 0.8003 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0609
  time to fit residues: 5.7169
Evaluate side-chains
  62 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 135 GLN
A 209 ASN
C  58 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.113349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.100104 restraints weight = 5219.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 1.61
r_work: 0.3054 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.1089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3999  Z= 0.158
  Angle     :  0.575   6.555   5431  Z= 0.310
  Chirality :  0.043   0.143    630
  Planarity :  0.004   0.034    665
  Dihedral  :  4.629  23.150    518
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  :  5.35 %
    Favored  : 92.33 %
  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:  1.39 (0.38), residues: 487
  helix:  1.48 (0.29), residues: 289
  sheet:  0.96 (0.64), residues: 58
  loop : -0.16 (0.57), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 319 
 TYR   0.016   0.002   TYR C 102 
 PHE   0.017   0.001   PHE C  27 
 TRP   0.012   0.001   TRP A 251 
 HIS   0.004   0.001   HIS A 180 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.16 ( 3998)
  covalent geometry    : angle       0.57499 /  0.31 ( 5429)
  SS BOND              : bond        0.00084 /  0.04 (    1)
  SS BOND              : angle       0.31687 /  0.17 (    2)
  hydrogen bonds       : bond        0.05555 /  3.77 (  256)
  hydrogen bonds       : angle       4.65068 /  3.47 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A  303 LYS cc_start: 0.8774 (tppt) cc_final: 0.8557 (tppt)
REVERT: A  407 ASN cc_start: 0.8459 (t0) cc_final: 0.8100 (t0)
  outliers start: 10
  outliers final: 6
  residues processed: 66
  average time/residue: 0.0676
  time to fit residues: 5.6786
Evaluate side-chains
  61 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  233 MET
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   39 GLN
Chi-restraints excluded: chain C residue   82 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 36 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  73 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.113707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.100641 restraints weight = 5115.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.59
r_work: 0.3061 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8855
moved from start:          0.1340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3999  Z= 0.143
  Angle     :  0.540   6.485   5431  Z= 0.291
  Chirality :  0.043   0.142    630
  Planarity :  0.004   0.034    665
  Dihedral  :  4.466  24.704    518
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  :  9.30 %
    Favored  : 88.37 %
  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:  1.72 (0.38), residues: 487
  helix:  1.74 (0.29), residues: 289
  sheet:  1.06 (0.64), residues: 58
  loop :  0.02 (0.59), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 319 
 TYR   0.019   0.001   TYR C 102 
 PHE   0.016   0.001   PHE C  27 
 TRP   0.013   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A 180 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.14 ( 3998)
  covalent geometry    : angle       0.54005 /  0.29 ( 5429)
  SS BOND              : bond        0.00102 /  0.05 (    1)
  SS BOND              : angle       0.30769 /  0.17 (    2)
  hydrogen bonds       : bond        0.05029 /  3.43 (  256)
  hydrogen bonds       : angle       4.35056 /  3.22 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
REVERT: A  303 LYS cc_start: 0.8781 (tppt) cc_final: 0.8558 (tppt)
  outliers start: 10
  outliers final: 7
  residues processed: 62
  average time/residue: 0.0644
  time to fit residues: 5.1631
Evaluate side-chains
  63 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  273 ASP
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   82 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 45 optimal weight:    0.0570
   chunk 6 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0570
   chunk 14 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.5216

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.114387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.101210 restraints weight = 5127.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 1.57
r_work: 0.3098 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3999  Z= 0.126
  Angle     :  0.520   6.761   5431  Z= 0.277
  Chirality :  0.042   0.147    630
  Planarity :  0.004   0.034    665
  Dihedral  :  4.375  26.282    518
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 13.02 %
    Favored  : 84.65 %
  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:  1.92 (0.38), residues: 487
  helix:  1.94 (0.29), residues: 288
  sheet:  1.10 (0.65), residues: 58
  loop :  0.02 (0.59), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 319 
 TYR   0.018   0.001   TYR C 102 
 PHE   0.014   0.001   PHE C  27 
 TRP   0.012   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A 180 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.13 ( 3998)
  covalent geometry    : angle       0.51963 /  0.28 ( 5429)
  SS BOND              : bond        0.00089 /  0.05 (    1)
  SS BOND              : angle       0.29189 /  0.16 (    2)
  hydrogen bonds       : bond        0.04573 /  3.13 (  256)
  hydrogen bonds       : angle       4.22932 /  3.13 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8225 (m-30)
REVERT: A  303 LYS cc_start: 0.8783 (tppt) cc_final: 0.8549 (tppt)
REVERT: C   88 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6560 (pm20)
  outliers start: 10
  outliers final: 7
  residues processed: 64
  average time/residue: 0.0598
  time to fit residues: 5.0129
Evaluate side-chains
  68 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   88 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 13 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0770
   chunk 5 optimal weight:    0.2980
   chunk 36 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 39 optimal weight:    5.9990
   overall best weight:    0.4938

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.117264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.103711 restraints weight = 5115.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 1.57
r_work: 0.3130 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8850
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3999  Z= 0.124
  Angle     :  0.513   6.462   5431  Z= 0.274
  Chirality :  0.042   0.153    630
  Planarity :  0.004   0.035    665
  Dihedral  :  4.330  26.925    518
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 13.95 %
    Favored  : 83.02 %
  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:  1.93 (0.38), residues: 487
  helix:  1.90 (0.29), residues: 294
  sheet:  1.10 (0.65), residues: 58
  loop :  0.07 (0.60), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 319 
 TYR   0.015   0.001   TYR C 102 
 PHE   0.014   0.001   PHE C  27 
 TRP   0.012   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A 180 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.12 ( 3998)
  covalent geometry    : angle       0.51319 /  0.27 ( 5429)
  SS BOND              : bond        0.00094 /  0.05 (    1)
  SS BOND              : angle       0.29109 /  0.16 (    2)
  hydrogen bonds       : bond        0.04486 /  3.07 (  256)
  hydrogen bonds       : angle       4.15414 /  3.06 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8286 (m-30)
REVERT: C   88 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6548 (pm20)
  outliers start: 13
  outliers final: 7
  residues processed: 67
  average time/residue: 0.0588
  time to fit residues: 5.2435
Evaluate side-chains
  64 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   88 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 30 optimal weight:    0.5980
   chunk 46 optimal weight:    5.9990
   chunk 13 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 250 ASN
A 358 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.116228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.102432 restraints weight = 5153.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.60
r_work: 0.3114 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8867
moved from start:          0.1767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3999  Z= 0.133
  Angle     :  0.525   7.311   5431  Z= 0.278
  Chirality :  0.042   0.160    630
  Planarity :  0.004   0.035    665
  Dihedral  :  4.314  27.028    518
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 13.49 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.38), residues: 487
  helix:  1.96 (0.29), residues: 293
  sheet:  1.08 (0.65), residues: 58
  loop :  0.14 (0.60), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 291 
 TYR   0.018   0.001   TYR C 102 
 PHE   0.013   0.001   PHE C  27 
 TRP   0.010   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A 180 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.13 ( 3998)
  covalent geometry    : angle       0.52467 /  0.28 ( 5429)
  SS BOND              : bond        0.00190 /  0.10 (    1)
  SS BOND              : angle       0.42849 /  0.23 (    2)
  hydrogen bonds       : bond        0.04561 /  3.13 (  256)
  hydrogen bonds       : angle       4.12719 /  3.04 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8242 (m-30)
REVERT: C   88 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6530 (pm20)
  outliers start: 15
  outliers final: 10
  residues processed: 66
  average time/residue: 0.0581
  time to fit residues: 5.0763
Evaluate side-chains
  67 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   88 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0970
   chunk 12 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 5 optimal weight:    0.3980
   chunk 47 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.6178

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.115147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.101414 restraints weight = 5187.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 1.62
r_work: 0.3103 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8858
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3999  Z= 0.132
  Angle     :  0.521   6.532   5431  Z= 0.278
  Chirality :  0.042   0.160    630
  Planarity :  0.004   0.035    665
  Dihedral  :  4.306  27.210    518
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 14.65 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.38), residues: 487
  helix:  1.99 (0.29), residues: 293
  sheet:  1.13 (0.66), residues: 58
  loop :  0.18 (0.60), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 291 
 TYR   0.017   0.001   TYR C 102 
 PHE   0.013   0.001   PHE C  27 
 TRP   0.010   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A 180 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 3998)
  covalent geometry    : angle       0.52089 /  0.28 ( 5429)
  SS BOND              : bond        0.00072 /  0.04 (    1)
  SS BOND              : angle       0.38440 /  0.20 (    2)
  hydrogen bonds       : bond        0.04552 /  3.11 (  256)
  hydrogen bonds       : angle       4.09185 /  3.01 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 54
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8257 (m-30)
REVERT: C   88 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6583 (pm20)
  outliers start: 15
  outliers final: 11
  residues processed: 63
  average time/residue: 0.0614
  time to fit residues: 5.0443
Evaluate side-chains
  68 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   88 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 39 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.8584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.112439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.099089 restraints weight = 5138.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 1.58
r_work: 0.3065 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8883
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3999  Z= 0.154
  Angle     :  0.543   7.468   5431  Z= 0.289
  Chirality :  0.043   0.164    630
  Planarity :  0.004   0.035    665
  Dihedral  :  4.369  27.033    518
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 15.58 %
    Favored  : 80.93 %
  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:  1.92 (0.38), residues: 487
  helix:  1.91 (0.29), residues: 294
  sheet:  1.03 (0.65), residues: 59
  loop :  0.06 (0.59), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 291 
 TYR   0.018   0.001   TYR C 102 
 PHE   0.014   0.001   PHE C  27 
 TRP   0.007   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A 180 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.15 ( 3998)
  covalent geometry    : angle       0.54326 /  0.29 ( 5429)
  SS BOND              : bond        0.00201 /  0.11 (    1)
  SS BOND              : angle       0.52321 /  0.29 (    2)
  hydrogen bonds       : bond        0.04851 /  3.33 (  256)
  hydrogen bonds       : angle       4.13295 /  3.04 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8277 (m-30)
REVERT: A  187 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8480 (tttm)
REVERT: C   88 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6681 (pm20)
  outliers start: 15
  outliers final: 10
  residues processed: 67
  average time/residue: 0.0807
  time to fit residues: 6.8856
Evaluate side-chains
  70 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  187 LYS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   88 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 44 optimal weight:    0.3980
   chunk 13 optimal weight:    0.5980
   chunk 7 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.6180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.115928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.102079 restraints weight = 5175.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.60
r_work: 0.3098 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8860
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3999  Z= 0.134
  Angle     :  0.530   7.294   5431  Z= 0.283
  Chirality :  0.042   0.167    630
  Planarity :  0.004   0.035    665
  Dihedral  :  4.345  27.243    518
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.05 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.38), residues: 487
  helix:  1.99 (0.29), residues: 294
  sheet:  0.95 (0.65), residues: 59
  loop :  0.10 (0.59), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  66 
 TYR   0.017   0.001   TYR C 102 
 PHE   0.012   0.001   PHE C  27 
 TRP   0.010   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A 180 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.13 ( 3998)
  covalent geometry    : angle       0.53027 /  0.28 ( 5429)
  SS BOND              : bond        0.00117 /  0.06 (    1)
  SS BOND              : angle       0.46471 /  0.26 (    2)
  hydrogen bonds       : bond        0.04549 /  3.12 (  256)
  hydrogen bonds       : angle       4.09050 /  3.01 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8268 (m-30)
REVERT: A  187 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8451 (tttm)
REVERT: C   19 ARG cc_start: 0.8592 (mtp85) cc_final: 0.8360 (mtp85)
  outliers start: 13
  outliers final: 11
  residues processed: 64
  average time/residue: 0.0709
  time to fit residues: 5.7598
Evaluate side-chains
  70 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  187 LYS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue  107 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 20 optimal weight:    0.0770
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.6138

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.116143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.102255 restraints weight = 5184.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 1.61
r_work: 0.3099 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8857
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3999  Z= 0.133
  Angle     :  0.526   7.238   5431  Z= 0.280
  Chirality :  0.042   0.164    630
  Planarity :  0.004   0.035    665
  Dihedral  :  4.310  27.981    518
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.05 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.05 (0.38), residues: 487
  helix:  2.01 (0.29), residues: 294
  sheet:  1.04 (0.65), residues: 59
  loop :  0.13 (0.60), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  66 
 TYR   0.016   0.001   TYR C 102 
 PHE   0.013   0.001   PHE C  27 
 TRP   0.010   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A 180 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 ( 3998)
  covalent geometry    : angle       0.52549 /  0.28 ( 5429)
  SS BOND              : bond        0.00143 /  0.08 (    1)
  SS BOND              : angle       0.57696 /  0.33 (    2)
  hydrogen bonds       : bond        0.04516 /  3.10 (  256)
  hydrogen bonds       : angle       4.07054 /  3.00 (  750)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A  113 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8251 (m-30)
REVERT: A  187 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8442 (tttm)
REVERT: A  303 LYS cc_start: 0.8771 (tppt) cc_final: 0.8168 (pttt)
REVERT: A  375 LYS cc_start: 0.8478 (ttmm) cc_final: 0.8125 (mmtm)
  outliers start: 13
  outliers final: 11
  residues processed: 65
  average time/residue: 0.0609
  time to fit residues: 5.1922
Evaluate side-chains
  71 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  187 LYS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   43 LYS
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue  107 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 14 optimal weight:    0.0060
   chunk 25 optimal weight:    0.5980
   chunk 7 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0970
   chunk 30 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 18 optimal weight:    0.3980
   chunk 29 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.3794

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.117378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.103704 restraints weight = 5181.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 1.62
r_work: 0.3104 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8820
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   3999  Z= 0.117
  Angle     :  0.511   7.369   5431  Z= 0.271
  Chirality :  0.041   0.166    630
  Planarity :  0.004   0.035    665
  Dihedral  :  4.271  28.861    518
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 16.05 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.18 (0.38), residues: 487
  helix:  2.14 (0.29), residues: 293
  sheet:  1.14 (0.65), residues: 59
  loop :  0.09 (0.60), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  66 
 TYR   0.014   0.001   TYR C 102 
 PHE   0.012   0.001   PHE C  27 
 TRP   0.012   0.001   TRP A 251 
 HIS   0.002   0.001   HIS A 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.12 ( 3998)
  covalent geometry    : angle       0.51068 /  0.27 ( 5429)
  SS BOND              : bond        0.00048 /  0.03 (    1)
  SS BOND              : angle       0.45588 /  0.26 (    2)
  hydrogen bonds       : bond        0.04219 /  2.92 (  256)
  hydrogen bonds       : angle       4.01100 /  2.95 (  750)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1090.44 seconds
wall clock time: 19 minutes 30.25 seconds (1170.25 seconds total)