Starting phenix.real_space_refine
on Wed Sep 17 03:56:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xd1_38262/09_2025/8xd1_38262_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xd1_38262/09_2025/8xd1_38262.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xd1_38262/09_2025/8xd1_38262.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xd1_38262/09_2025/8xd1_38262.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xd1_38262/09_2025/8xd1_38262_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xd1_38262/09_2025/8xd1_38262_neut.cif"
  }
  resolution = 2.96
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      14      5.16       5
     C    2097      2.51       5
     N     562      2.21       5
     O     631      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3307
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3267
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 416, 3261
          Classifications: {'peptide': 416}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 395}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
      Conformer: "B"
        Number of residues, atoms: 416, 3261
          Classifications: {'peptide': 416}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 395}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
          bond proxies already assigned to first conformer: 3327
    Chain: "A"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 40
          Unusual residues: {'NAP': 1}
          Classifications: {'undetermined': 1, 'water': 9}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 40
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'NAP:plan-2': 1, 'NAP:plan-4': 1}
          Unresolved non-hydrogen planarities: 12
  Time building chain proxies: 1.71, per 1000 atoms: 0.52
  Number of scatterers: 3307
  At special positions: 0
  Unit cell: (67.68, 73.696, 71.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P       3     15.00
     O     631      8.00
     N     562      7.00
     C    2097      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.27
  Conformation dependent library (CDL) restraints added in 261.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  760

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 2 sheets defined
      54.8% alpha, 13.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 19
    Processing helix  chain 'A' and resid 24 through 32
    Processing helix  chain 'A' and resid 79 through 97
      removed outlier: 3.523A  pdb=" N   TRP A  92 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   VAL A  97 " --> pdb=" O   LYS A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 115
    Processing helix  chain 'A' and resid 116 through 132
    Processing helix  chain 'A' and resid 133 through 135
      No H-bonds generated for 'chain 'A' and resid 133 through 135'
    Processing helix  chain 'A' and resid 149 through 165
    Processing helix  chain 'A' and resid 169 through 174
      removed outlier: 3.537A  pdb=" N   VAL A 173 " --> pdb=" O   ALA A 170 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE A 174 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 207
    Processing helix  chain 'A' and resid 223 through 235
    Processing helix  chain 'A' and resid 256 through 268
      removed outlier: 3.571A  pdb=" N   VAL A 260 " --> pdb=" O   ASP A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 287
    Processing helix  chain 'A' and resid 323 through 333
    Processing helix  chain 'A' and resid 339 through 344
      removed outlier: 3.607A  pdb=" N   ASN A 344 " --> pdb=" O   ASP A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 361
    Processing helix  chain 'A' and resid 365 through 392
    Processing helix  chain 'A' and resid 394 through 415
    Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45
      removed outlier: 4.543A  pdb=" N   THR A  55 " --> pdb=" O   ILE A 109 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   GLY A 103 " --> pdb=" O   HIS A  61 " (cutoff:3.500A)
      removed outlier: 5.187A  pdb=" N   LYS A  69 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   GLY A 106 " --> pdb=" O   LYS A  69 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   GLY A  71 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   ILE A 108 " --> pdb=" O   GLY A  71 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ARG A  73 " --> pdb=" O   ILE A 108 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   THR A  68 " --> pdb=" O   ILE A 141 " (cutoff:3.500A)
      removed outlier: 8.087A  pdb=" N   ALA A 143 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   GLY A  70 " --> pdb=" O   ALA A 143 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279
      removed outlier: 6.318A  pdb=" N   ILE A 215 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ALA A 241 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   LYS A 214 " --> pdb=" O   VAL A 291 " (cutoff:3.500A)
      removed outlier: 8.277A  pdb=" N   ALA A 293 " --> pdb=" O   LYS A 214 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   ALA A 216 " --> pdb=" O   ALA A 293 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   VAL A 314 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)

    183 hydrogen bonds defined for protein.
    530 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: 0.50

  Time building geometry restraints manager: 0.38 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: 584
        1.32 -     1.44: 841
        1.44 -     1.57: 1918
        1.57 -     1.69: 4
        1.69 -     1.81: 27
  Bond restraints: 3374
  Sorted by residual:
  bond pdb=" O2B NAP A 500 "
       pdb=" P2B NAP A 500 "
    ideal  model  delta    sigma   weight residual
    1.736  1.567  0.169 2.00e-02 2.50e+03 7.17e+01
  bond pdb=" C4A NAP A 500 "
       pdb=" N3A NAP A 500 "
    ideal  model  delta    sigma   weight residual
    1.332  1.439 -0.107 2.00e-02 2.50e+03 2.85e+01
  bond pdb=" C6A NAP A 500 "
       pdb=" N6A NAP A 500 "
    ideal  model  delta    sigma   weight residual
    1.335  1.436 -0.101 2.00e-02 2.50e+03 2.56e+01
  bond pdb=" C8A NAP A 500 "
       pdb=" N7A NAP A 500 "
    ideal  model  delta    sigma   weight residual
    1.301  1.399 -0.098 2.00e-02 2.50e+03 2.42e+01
  bond pdb=" N   LYS A 204 "
       pdb=" CA BLYS A 204 "
    ideal  model  delta    sigma   weight residual
    1.459  1.402  0.057 1.23e-02 6.61e+03 2.16e+01
  ... (remaining 3369 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 4491
        2.41 -     4.82: 71
        4.82 -     7.23: 12
        7.23 -     9.64: 7
        9.64 -    12.05: 2
  Bond angle restraints: 4583
  Sorted by residual:
  angle pdb=" N   GLN A 234 "
        pdb=" CA  GLN A 234 "
        pdb=" C   GLN A 234 "
      ideal   model   delta    sigma   weight residual
     111.07  116.91   -5.84 1.07e+00 8.73e-01 2.98e+01
  angle pdb=" N   VAL A 270 "
        pdb=" CA  VAL A 270 "
        pdb=" C   VAL A 270 "
      ideal   model   delta    sigma   weight residual
     106.21  111.30   -5.09 1.07e+00 8.73e-01 2.26e+01
  angle pdb=" C   ASP A   5 "
        pdb=" N   PRO A   6 "
        pdb=" CA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     118.85  123.76   -4.91 1.09e+00 8.42e-01 2.03e+01
  angle pdb=" N   ARG A 396 "
        pdb=" CA  ARG A 396 "
        pdb=" C   ARG A 396 "
      ideal   model   delta    sigma   weight residual
     111.07  106.32    4.75 1.07e+00 8.73e-01 1.97e+01
  angle pdb=" O1A NAP A 500 "
        pdb=" PA  NAP A 500 "
        pdb=" O2A NAP A 500 "
      ideal   model   delta    sigma   weight residual
     121.77  109.72   12.05 3.00e+00 1.11e-01 1.61e+01
  ... (remaining 4578 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 1781
       17.85 -    35.71: 165
       35.71 -    53.56: 60
       53.56 -    71.41: 26
       71.41 -    89.27: 8
  Dihedral angle restraints: 2040
    sinusoidal: 847
      harmonic: 1193
  Sorted by residual:
  dihedral pdb=" CB  GLU A 286 "
           pdb=" CG  GLU A 286 "
           pdb=" CD  GLU A 286 "
           pdb=" OE1 GLU A 286 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   84.44  -84.44     1      3.00e+01 1.11e-03 9.63e+00
  dihedral pdb=" CB  GLU A  78 "
           pdb=" CG  GLU A  78 "
           pdb=" CD  GLU A  78 "
           pdb=" OE1 GLU A  78 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -84.26   84.26     1      3.00e+01 1.11e-03 9.60e+00
  dihedral pdb=" N   ASP A 290 "
           pdb=" CA  ASP A 290 "
           pdb=" CB  ASP A 290 "
           pdb=" CG  ASP A 290 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.64   59.64     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 2037 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 417
       0.059 -    0.118: 76
       0.118 -    0.177: 3
       0.177 -    0.236: 1
       0.236 -    0.295: 1
  Chirality restraints: 498
  Sorted by residual:
  chirality pdb=" C2B NAP A 500 "
            pdb=" C1B NAP A 500 "
            pdb=" C3B NAP A 500 "
            pdb=" O2B NAP A 500 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.46   -0.29 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" CA  GLN A 234 "
            pdb=" N   GLN A 234 "
            pdb=" C   GLN A 234 "
            pdb=" CB  GLN A 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.18e-01
  chirality pdb=" C4B NAP A 500 "
            pdb=" C3B NAP A 500 "
            pdb=" C5B NAP A 500 "
            pdb=" O4B NAP A 500 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.54   -2.40   -0.14 2.00e-01 2.50e+01 5.21e-01
  ... (remaining 495 not shown)

  Planarity restraints: 583
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 338 "    0.047 5.00e-02 4.00e+02   7.08e-02 8.01e+00
        pdb=" N   PRO A 339 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO A 339 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 339 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 251 "   -0.046 5.00e-02 4.00e+02   7.05e-02 7.95e+00
        pdb=" N   PRO A 252 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO A 252 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 252 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 149 "   -0.026 5.00e-02 4.00e+02   3.93e-02 2.48e+00
        pdb=" N   PRO A 150 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 150 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 150 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 580 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.88: 1210
        2.88 -     3.38: 3145
        3.38 -     3.89: 5768
        3.89 -     4.39: 6487
        4.39 -     4.90: 11053
  Nonbonded interactions: 27663
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 105 "
            pdb=" OD2 ASP A 145 "
     model   vdw
     2.373 3.120
  nonbonded pdb=" NH2 ARG A 118 "
            pdb=" OE1 GLU A 121 "
     model   vdw
     2.516 3.120
  nonbonded pdb=" O   ILE A 174 "
            pdb=" NZ  LYS A 177 "
     model   vdw
     2.523 3.120
  nonbonded pdb=" O   ILE A 109 "
            pdb=" O   HOH A 601 "
     model   vdw
     2.524 3.040
  nonbonded pdb=" O   ALA A 223 "
            pdb=" OG1 THR A 227 "
     model   vdw
     2.528 3.040
  ... (remaining 27658 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=0.50 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:             1.550
  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:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.260
  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:9.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
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   0.169   3374  Z= 0.379
  Angle     :  0.830  12.050   4583  Z= 0.465
  Chirality :  0.046   0.295    498
  Planarity :  0.006   0.071    583
  Dihedral  : 18.201  89.266   1280
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  6.49 %
    Allowed  :  4.42 %
    Favored  : 89.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.43), residues: 415
  helix:  1.98 (0.36), residues: 209
  sheet: -0.69 (0.78), residues: 50
  loop : -0.87 (0.50), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 246 
 TYR   0.006   0.001   TYR A 408 
 PHE   0.008   0.001   PHE A 381 
 TRP   0.008   0.001   TRP A  30 
 HIS   0.002   0.000   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00718 ( 3374)
  covalent geometry    : angle       0.82956 ( 4583)
  hydrogen bonds       : bond        0.12701 (  183)
  hydrogen bonds       : angle       6.05287 (  530)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.8157 (mp) cc_final: 0.7881 (mp)
REVERT: A  290 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6897 (m-30)
  outliers start: 21
  outliers final: 4
  residues processed: 80
  average time/residue: 0.6989
  time to fit residues: 57.2042
Evaluate side-chains
  59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 MET
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  265 ARG
Chi-restraints excluded: chain A residue  290 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
A  13 GLN
A 218 GLN
A 234 GLN
A 337 GLN
A 388 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.138976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.104416 restraints weight = 6097.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 2.28
r_work: 0.2882 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2675
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2675 r_free = 0.2675    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2675 r_free = 0.2675    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8625
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3374  Z= 0.146
  Angle     :  0.548   5.944   4583  Z= 0.282
  Chirality :  0.043   0.126    498
  Planarity :  0.006   0.064    583
  Dihedral  : 11.339  60.993    504
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.63 %
    Favored  : 82.30 %
  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 aren not related in a simple way.
  whole:  1.29 (0.44), residues: 415
  helix:  2.18 (0.37), residues: 211
  sheet: -0.05 (0.72), residues: 63
  loop : -0.76 (0.54), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 370 
 TYR   0.014   0.001   TYR A 250 
 PHE   0.008   0.001   PHE A 381 
 TRP   0.022   0.001   TRP A 263 
 HIS   0.008   0.002   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 3374)
  covalent geometry    : angle       0.54762 ( 4583)
  hydrogen bonds       : bond        0.04241 (  183)
  hydrogen bonds       : angle       4.69162 (  530)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.149 
Fit side-chains
   revert: symmetry clash
REVERT: A  271 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.7050 (ptmt)
  outliers start: 6
  outliers final: 2
  residues processed: 66
  average time/residue: 0.6143
  time to fit residues: 41.6262
Evaluate side-chains
  60 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  271 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 38 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 15 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 31 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 24 optimal weight:    9.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 218 GLN
A 234 GLN
** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 388 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.138846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.104100 restraints weight = 6112.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 2.27
r_work: 0.2880 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2726
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2726 r_free = 0.2726    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2726 r_free = 0.2726    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2726
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3374  Z= 0.136
  Angle     :  0.514   6.142   4583  Z= 0.265
  Chirality :  0.043   0.124    498
  Planarity :  0.006   0.057    583
  Dihedral  :  9.384  55.915    493
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 16.81 %
    Favored  : 81.12 %
  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 aren not related in a simple way.
  whole:  1.37 (0.44), residues: 415
  helix:  2.24 (0.37), residues: 210
  sheet: -0.15 (0.69), residues: 68
  loop : -0.62 (0.56), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 370 
 TYR   0.008   0.001   TYR A 363 
 PHE   0.009   0.001   PHE A 381 
 TRP   0.019   0.001   TRP A 263 
 HIS   0.007   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 3374)
  covalent geometry    : angle       0.51401 ( 4583)
  hydrogen bonds       : bond        0.03900 (  183)
  hydrogen bonds       : angle       4.42841 (  530)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.8444 (mp) cc_final: 0.7838 (mp)
  outliers start: 6
  outliers final: 3
  residues processed: 65
  average time/residue: 0.5872
  time to fit residues: 39.2231
Evaluate side-chains
  59 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  270 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 12 optimal weight:    0.7980
   chunk 18 optimal weight:    0.3980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 388 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.141707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.104963 restraints weight = 11045.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 3.15
r_work: 0.2864 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2884
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2884 r_free = 0.2884    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2883 r_free = 0.2883    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2883
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3374  Z= 0.101
  Angle     :  0.499   6.534   4583  Z= 0.250
  Chirality :  0.042   0.126    498
  Planarity :  0.005   0.053    583
  Dihedral  :  8.915  59.892    493
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 18.58 %
    Favored  : 80.53 %
  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 aren not related in a simple way.
  whole:  1.44 (0.44), residues: 415
  helix:  2.35 (0.36), residues: 210
  sheet: -0.09 (0.70), residues: 67
  loop : -0.70 (0.55), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 370 
 TYR   0.022   0.001   TYR A 250 
 PHE   0.008   0.001   PHE A 381 
 TRP   0.011   0.001   TRP A 263 
 HIS   0.006   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 3374)
  covalent geometry    : angle       0.49871 ( 4583)
  hydrogen bonds       : bond        0.03336 (  183)
  hydrogen bonds       : angle       4.19532 (  530)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.8301 (mp) cc_final: 0.7687 (mp)
  outliers start: 2
  outliers final: 2
  residues processed: 58
  average time/residue: 0.5796
  time to fit residues: 34.5896
Evaluate side-chains
  54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  270 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    0.0870
   chunk 30 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0570
   chunk 37 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   chunk 17 optimal weight:    0.1980
   chunk 39 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
A 218 GLN
A 267 HIS
A 388 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.144739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.109853 restraints weight = 6215.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 2.31
r_work: 0.2957 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2838 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2779
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2779 r_free = 0.2779    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2779 r_free = 0.2779    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3374  Z= 0.089
  Angle     :  0.476   6.754   4583  Z= 0.239
  Chirality :  0.042   0.131    498
  Planarity :  0.005   0.050    583
  Dihedral  :  7.532  59.417    491
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 20.35 %
    Favored  : 78.47 %
  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 aren not related in a simple way.
  whole:  1.52 (0.44), residues: 415
  helix:  2.41 (0.36), residues: 210
  sheet: -0.01 (0.71), residues: 67
  loop : -0.67 (0.55), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 370 
 TYR   0.006   0.001   TYR A 408 
 PHE   0.007   0.001   PHE A 381 
 TRP   0.011   0.001   TRP A  92 
 HIS   0.005   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00191 ( 3374)
  covalent geometry    : angle       0.47641 ( 4583)
  hydrogen bonds       : bond        0.02995 (  183)
  hydrogen bonds       : angle       4.01029 (  530)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.8359 (mp) cc_final: 0.7698 (mp)
  outliers start: 3
  outliers final: 2
  residues processed: 62
  average time/residue: 0.6120
  time to fit residues: 38.9117
Evaluate side-chains
  57 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  270 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 13 optimal weight:    0.4980
   chunk 12 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 34 optimal weight:    7.9990
   chunk 1 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 218 GLN
A 388 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.142843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.106489 restraints weight = 11060.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 3.10
r_work: 0.2884 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2851
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2851
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   3374  Z= 0.095
  Angle     :  0.482   7.548   4583  Z= 0.242
  Chirality :  0.042   0.128    498
  Planarity :  0.005   0.048    583
  Dihedral  :  6.635  54.391    491
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 21.53 %
    Favored  : 76.40 %
  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 aren not related in a simple way.
  whole:  1.63 (0.44), residues: 415
  helix:  2.48 (0.36), residues: 210
  sheet:  0.02 (0.71), residues: 67
  loop : -0.58 (0.55), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 370 
 TYR   0.022   0.001   TYR A 250 
 PHE   0.008   0.001   PHE A 381 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.005   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 3374)
  covalent geometry    : angle       0.48228 ( 4583)
  hydrogen bonds       : bond        0.03118 (  183)
  hydrogen bonds       : angle       4.00737 (  530)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.8268 (mp) cc_final: 0.7649 (mp)
REVERT: A  263 TRP cc_start: 0.6405 (t60) cc_final: 0.5982 (t60)
REVERT: A  266 GLU cc_start: 0.8662 (tt0) cc_final: 0.8009 (pt0)
REVERT: A  310 LYS cc_start: 0.8139 (mttp) cc_final: 0.7934 (mttp)
  outliers start: 6
  outliers final: 3
  residues processed: 61
  average time/residue: 0.5830
  time to fit residues: 36.5333
Evaluate side-chains
  56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  270 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 26 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 12 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 218 GLN
A 388 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.143223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.108201 restraints weight = 7765.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 2.55
r_work: 0.2922 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2801 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2749
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2749 r_free = 0.2749    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2749 r_free = 0.2749    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2749
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3374  Z= 0.101
  Angle     :  0.490   7.801   4583  Z= 0.246
  Chirality :  0.042   0.125    498
  Planarity :  0.005   0.048    583
  Dihedral  :  6.404  53.635    491
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 22.42 %
    Favored  : 76.40 %
  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 aren not related in a simple way.
  whole:  1.66 (0.44), residues: 415
  helix:  2.52 (0.36), residues: 210
  sheet: -0.01 (0.71), residues: 67
  loop : -0.56 (0.55), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 370 
 TYR   0.006   0.001   TYR A 363 
 PHE   0.008   0.001   PHE A 381 
 TRP   0.009   0.001   TRP A 263 
 HIS   0.009   0.002   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 3374)
  covalent geometry    : angle       0.48990 ( 4583)
  hydrogen bonds       : bond        0.03187 (  183)
  hydrogen bonds       : angle       4.08787 (  530)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.8344 (mp) cc_final: 0.7697 (mp)
REVERT: A  262 LYS cc_start: 0.8666 (tttp) cc_final: 0.8363 (ptmm)
  outliers start: 3
  outliers final: 2
  residues processed: 56
  average time/residue: 0.5920
  time to fit residues: 34.1365
Evaluate side-chains
  54 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  270 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    0.5980
   chunk 20 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 218 GLN
A 388 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.141542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.105988 restraints weight = 7707.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 2.59
r_work: 0.2857 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2736 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2784
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3374  Z= 0.106
  Angle     :  0.490   7.814   4583  Z= 0.247
  Chirality :  0.042   0.123    498
  Planarity :  0.005   0.047    583
  Dihedral  :  6.184  50.668    491
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 23.60 %
    Favored  : 75.52 %
  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 aren not related in a simple way.
  whole:  1.69 (0.44), residues: 415
  helix:  2.53 (0.37), residues: 210
  sheet: -0.04 (0.71), residues: 67
  loop : -0.50 (0.56), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 370 
 TYR   0.021   0.001   TYR A 250 
 PHE   0.008   0.001   PHE A 381 
 TRP   0.011   0.001   TRP A 263 
 HIS   0.005   0.002   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 3374)
  covalent geometry    : angle       0.48992 ( 4583)
  hydrogen bonds       : bond        0.03281 (  183)
  hydrogen bonds       : angle       4.10481 (  530)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 56
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.8372 (mp) cc_final: 0.7736 (mp)
REVERT: A  262 LYS cc_start: 0.8662 (tttp) cc_final: 0.8350 (ptmm)
REVERT: A  266 GLU cc_start: 0.8701 (tt0) cc_final: 0.8390 (pt0)
  outliers start: 2
  outliers final: 2
  residues processed: 58
  average time/residue: 0.6227
  time to fit residues: 37.1131
Evaluate side-chains
  53 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  270 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 388 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.140789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.104619 restraints weight = 10039.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 2.95
r_work: 0.2774 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2845
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2845
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3374  Z= 0.119
  Angle     :  0.514   7.782   4583  Z= 0.260
  Chirality :  0.043   0.124    498
  Planarity :  0.005   0.047    583
  Dihedral  :  6.131  49.097    491
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 23.60 %
    Favored  : 75.22 %
  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 aren not related in a simple way.
  whole:  1.67 (0.44), residues: 415
  helix:  2.51 (0.37), residues: 210
  sheet: -0.07 (0.70), residues: 67
  loop : -0.48 (0.56), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 370 
 TYR   0.008   0.001   TYR A 363 
 PHE   0.009   0.001   PHE A 381 
 TRP   0.013   0.001   TRP A 263 
 HIS   0.006   0.002   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3374)
  covalent geometry    : angle       0.51442 ( 4583)
  hydrogen bonds       : bond        0.03483 (  183)
  hydrogen bonds       : angle       4.16537 (  530)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.8273 (mp) cc_final: 0.7669 (mp)
REVERT: A  262 LYS cc_start: 0.8628 (tttp) cc_final: 0.8328 (ptmm)
REVERT: A  266 GLU cc_start: 0.8583 (tt0) cc_final: 0.8160 (pt0)
  outliers start: 3
  outliers final: 2
  residues processed: 58
  average time/residue: 0.6215
  time to fit residues: 37.0092
Evaluate side-chains
  56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  270 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0980
   chunk 8 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 234 GLN
A 388 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.141919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.105807 restraints weight = 10093.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 2.98
r_work: 0.2895 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2861
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2861 r_free = 0.2861    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2861 r_free = 0.2861    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2861
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   3374  Z= 0.097
  Angle     :  0.499   8.044   4583  Z= 0.251
  Chirality :  0.042   0.126    498
  Planarity :  0.005   0.050    583
  Dihedral  :  6.023  48.298    491
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 23.01 %
    Favored  : 76.11 %
  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 aren not related in a simple way.
  whole:  1.65 (0.44), residues: 415
  helix:  2.48 (0.36), residues: 210
  sheet: -0.05 (0.70), residues: 67
  loop : -0.48 (0.56), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 370 
 TYR   0.022   0.001   TYR A 250 
 PHE   0.009   0.001   PHE A 381 
 TRP   0.010   0.001   TRP A 263 
 HIS   0.005   0.002   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 3374)
  covalent geometry    : angle       0.49856 ( 4583)
  hydrogen bonds       : bond        0.03139 (  183)
  hydrogen bonds       : angle       4.08222 (  530)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.8296 (mp) cc_final: 0.7679 (mp)
REVERT: A  262 LYS cc_start: 0.8591 (tttp) cc_final: 0.8346 (tttm)
REVERT: A  266 GLU cc_start: 0.8438 (tt0) cc_final: 0.8041 (pt0)
  outliers start: 2
  outliers final: 1
  residues processed: 56
  average time/residue: 0.6262
  time to fit residues: 36.0066
Evaluate side-chains
  52 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0050
   chunk 20 optimal weight:    0.0770
   chunk 37 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0050
   overall best weight:    0.3566

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

Flipped N/Q/H residues before XYZ refinement:
A 388 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.145251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.110633 restraints weight = 6540.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 2.39
r_work: 0.2972 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2854
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2854
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3374  Z= 0.090
  Angle     :  0.488   8.322   4583  Z= 0.244
  Chirality :  0.042   0.127    498
  Planarity :  0.005   0.052    583
  Dihedral  :  5.873  47.188    491
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 23.30 %
    Favored  : 75.81 %
  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 aren not related in a simple way.
  whole:  1.69 (0.44), residues: 415
  helix:  2.51 (0.36), residues: 210
  sheet:  0.09 (0.71), residues: 67
  loop : -0.54 (0.56), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 370 
 TYR   0.006   0.001   TYR A 408 
 PHE   0.008   0.001   PHE A 381 
 TRP   0.009   0.001   TRP A 382 
 HIS   0.005   0.001   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 ( 3374)
  covalent geometry    : angle       0.48760 ( 4583)
  hydrogen bonds       : bond        0.02885 (  183)
  hydrogen bonds       : angle       4.01343 (  530)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1553.15 seconds
wall clock time: 27 minutes 26.25 seconds (1646.25 seconds total)