Starting phenix.real_space_refine
on Fri Oct 10 12:43:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p6x_17510/10_2025/8p6x_17510.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p6x_17510/10_2025/8p6x_17510.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p6x_17510/10_2025/8p6x_17510.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p6x_17510/10_2025/8p6x_17510.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p6x_17510/10_2025/8p6x_17510.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p6x_17510/10_2025/8p6x_17510.cif"
  }
  resolution = 1.9
  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=   0.001
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      31      5.16       5
     C    3315      2.51       5
     N     875      2.21       5
     O    1063      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5284
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "H"
      Number of atoms: 512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 512
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 5, 'TRANS': 59}
    Chain: "I"
      Number of atoms: 2281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2281
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 279, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 2291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2291
          Classifications: {'peptide': 287}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 268}
          Chain breaks: 2
    Chain: "J"
      Number of atoms: 56
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1, 28
          Unusual residues: {'NS9': 1}
          Classifications: {'undetermined': 1}
      Conformer: "B"
        Number of residues, atoms: 1, 28
          Unusual residues: {'NS9': 1}
          Classifications: {'undetermined': 1}
    Chain: "H"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 15
          Classifications: {'water': 15}
          Link IDs: {None: 14}
    Chain: "I"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 65
          Classifications: {'water': 65}
          Link IDs: {None: 64}
    Chain: "J"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 64
          Classifications: {'water': 64}
          Link IDs: {None: 63}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C11ANS9 J 401 " occ=0.51
      ... (54 atoms not shown)
      pdb=" O25BNS9 J 401 " occ=0.49
  Time building chain proxies: 1.15, per 1000 atoms: 0.22
  Number of scatterers: 5284
  At special positions: 0
  Unit cell: (84.7875, 94.05, 67.6875, 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      31     16.00
     O    1063      8.00
     N     875      7.00
     C    3315      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: 0.36
  Conformation dependent library (CDL) restraints added in 162.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1198

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 3 sheets defined
      61.5% alpha, 4.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'H' and resid 262 through 266
    Processing helix  chain 'H' and resid 270 through 275
    Processing helix  chain 'H' and resid 279 through 285
    Processing helix  chain 'H' and resid 288 through 302
      removed outlier: 3.819A  pdb=" N   ALA H 292 " --> pdb=" O   THR H 288 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 1 through 4
    Processing helix  chain 'I' and resid 5 through 11
    Processing helix  chain 'I' and resid 15 through 38
    Processing helix  chain 'I' and resid 49 through 70
    Processing helix  chain 'I' and resid 76 through 93
      removed outlier: 3.883A  pdb=" N   ASN I  93 " --> pdb=" O   ARG I  89 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 100 through 116
      removed outlier: 3.685A  pdb=" N   LEU I 106 " --> pdb=" O   ARG I 102 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 121 through 127
    Processing helix  chain 'I' and resid 132 through 154
      removed outlier: 4.674A  pdb=" N   LEU I 148 " --> pdb=" O   LEU I 144 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   LEU I 149 " --> pdb=" O   GLU I 145 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 163 through 178
    Processing helix  chain 'I' and resid 183 through 186
      removed outlier: 3.569A  pdb=" N   ILE I 186 " --> pdb=" O   ASN I 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'I' and resid 183 through 186'
    Processing helix  chain 'I' and resid 187 through 201
      removed outlier: 3.627A  pdb=" N   THR I 201 " --> pdb=" O   ARG I 197 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 202 through 206
    Processing helix  chain 'I' and resid 208 through 224
    Processing helix  chain 'I' and resid 228 through 234
      removed outlier: 4.044A  pdb=" N   LEU I 232 " --> pdb=" O   MET I 228 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 241 through 261
    Processing helix  chain 'I' and resid 266 through 284
      removed outlier: 3.582A  pdb=" N   VAL I 272 " --> pdb=" O   GLU I 268 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 56 through 68
      removed outlier: 3.901A  pdb=" N   GLU J  68 " --> pdb=" O   LYS J  64 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 98 through 104
    Processing helix  chain 'J' and resid 110 through 131
    Processing helix  chain 'J' and resid 139 through 141
      No H-bonds generated for 'chain 'J' and resid 139 through 141'
    Processing helix  chain 'J' and resid 155 through 159
      removed outlier: 4.415A  pdb=" N   LEU J 158 " --> pdb=" O   ASP J 155 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 175 through 179
    Processing helix  chain 'J' and resid 180 through 185
    Processing helix  chain 'J' and resid 192 through 209
      removed outlier: 3.518A  pdb=" N   ALA J 198 " --> pdb=" O   VAL J 194 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 217 through 230
    Processing helix  chain 'J' and resid 239 through 243
      removed outlier: 3.677A  pdb=" N   LEU J 243 " --> pdb=" O   MET J 240 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 256 through 261
    Processing helix  chain 'J' and resid 265 through 276
    Processing helix  chain 'J' and resid 285 through 292
    Processing helix  chain 'J' and resid 303 through 307
    Processing sheet with id=AA1, first strand: chain 'J' and resid 17 through 20
      removed outlier: 6.436A  pdb=" N   VAL J  26 " --> pdb=" O   LEU J  18 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   ASP J  92 " --> pdb=" O   LEU J  77 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   LEU J  77 " --> pdb=" O   ASP J  92 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 96 through 97
    Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 134

    272 hydrogen bonds defined for protein.
    759 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: 0.55

  Time building geometry restraints manager: 0.50 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1648
        1.34 -     1.46: 1220
        1.46 -     1.58: 2348
        1.58 -     1.70: 0
        1.70 -     1.82: 49
  Bond restraints: 5265
  Sorted by residual:
  bond pdb=" C3 BNS9 J 401 "
       pdb=" N10BNS9 J 401 "
    ideal  model  delta    sigma   weight residual
    1.335  1.445 -0.110 2.00e-02 2.50e+03 3.04e+01
  bond pdb=" C3 ANS9 J 401 "
       pdb=" N10ANS9 J 401 "
    ideal  model  delta    sigma   weight residual
    1.335  1.444 -0.109 2.00e-02 2.50e+03 3.00e+01
  bond pdb=" C5 BNS9 J 401 "
       pdb=" N18BNS9 J 401 "
    ideal  model  delta    sigma   weight residual
    1.355  1.450 -0.095 2.00e-02 2.50e+03 2.24e+01
  bond pdb=" C5 ANS9 J 401 "
       pdb=" N18ANS9 J 401 "
    ideal  model  delta    sigma   weight residual
    1.355  1.448 -0.093 2.00e-02 2.50e+03 2.17e+01
  bond pdb=" C7 ANS9 J 401 "
       pdb=" N2 ANS9 J 401 "
    ideal  model  delta    sigma   weight residual
    1.376  1.300  0.076 2.00e-02 2.50e+03 1.45e+01
  ... (remaining 5260 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 6978
        1.86 -     3.72: 115
        3.72 -     5.58: 26
        5.58 -     7.43: 5
        7.43 -     9.29: 2
  Bond angle restraints: 7126
  Sorted by residual:
  angle pdb=" CB  MET I 237 "
        pdb=" CG  MET I 237 "
        pdb=" SD  MET I 237 "
      ideal   model   delta    sigma   weight residual
     112.70  121.99   -9.29 3.00e+00 1.11e-01 9.60e+00
  angle pdb=" CA  GLU I 229 "
        pdb=" CB  GLU I 229 "
        pdb=" CG  GLU I 229 "
      ideal   model   delta    sigma   weight residual
     114.10  119.33   -5.23 2.00e+00 2.50e-01 6.85e+00
  angle pdb=" CA  TYR I  91 "
        pdb=" CB  TYR I  91 "
        pdb=" CG  TYR I  91 "
      ideal   model   delta    sigma   weight residual
     113.90  109.52    4.38 1.80e+00 3.09e-01 5.92e+00
  angle pdb=" CA  LEU J 219 "
        pdb=" CB  LEU J 219 "
        pdb=" CG  LEU J 219 "
      ideal   model   delta    sigma   weight residual
     116.30  124.77   -8.47 3.50e+00 8.16e-02 5.85e+00
  angle pdb=" CA  ARG I  28 "
        pdb=" CB  ARG I  28 "
        pdb=" CG  ARG I  28 "
      ideal   model   delta    sigma   weight residual
     114.10  118.90   -4.80 2.00e+00 2.50e-01 5.75e+00
  ... (remaining 7121 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.49: 2759
       17.49 -    34.98: 325
       34.98 -    52.46: 61
       52.46 -    69.95: 25
       69.95 -    87.44: 8
  Dihedral angle restraints: 3178
    sinusoidal: 1328
      harmonic: 1850
  Sorted by residual:
  dihedral pdb=" CA  TYR I  91 "
           pdb=" C   TYR I  91 "
           pdb=" N   LEU I  92 "
           pdb=" CA  LEU I  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.99   17.01     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CB  GLU J  95 "
           pdb=" CG  GLU J  95 "
           pdb=" CD  GLU J  95 "
           pdb=" OE1 GLU J  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.44  -87.44     1      3.00e+01 1.11e-03 1.02e+01
  dihedral pdb=" CG  ARG I 279 "
           pdb=" CD  ARG I 279 "
           pdb=" NE  ARG I 279 "
           pdb=" CZ  ARG I 279 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  131.87  -41.87     2      1.50e+01 4.44e-03 9.50e+00
  ... (remaining 3175 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 536
       0.037 -    0.074: 171
       0.074 -    0.111: 59
       0.111 -    0.149: 12
       0.149 -    0.186: 3
  Chirality restraints: 781
  Sorted by residual:
  chirality pdb=" C19BNS9 J 401 "
            pdb=" C20BNS9 J 401 "
            pdb=" C23BNS9 J 401 "
            pdb=" N18BNS9 J 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.60   -0.19 2.00e-01 2.50e+01 8.61e-01
  chirality pdb=" C19ANS9 J 401 "
            pdb=" C20ANS9 J 401 "
            pdb=" C23ANS9 J 401 "
            pdb=" N18ANS9 J 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.60   -0.18 2.00e-01 2.50e+01 8.45e-01
  chirality pdb=" C20ANS9 J 401 "
            pdb=" C19ANS9 J 401 "
            pdb=" C21ANS9 J 401 "
            pdb=" O25ANS9 J 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.52    0.16 2.00e-01 2.50e+01 6.35e-01
  ... (remaining 778 not shown)

  Planarity restraints: 906
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG I 165 "    0.024 5.00e-02 4.00e+02   3.64e-02 2.13e+00
        pdb=" N   PRO I 166 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO I 166 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO I 166 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA J 198 "    0.007 2.00e-02 2.50e+03   1.32e-02 1.74e+00
        pdb=" C   ALA J 198 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   ALA J 198 "    0.009 2.00e-02 2.50e+03
        pdb=" N   VAL J 199 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL J 199 "    0.006 2.00e-02 2.50e+03   1.29e-02 1.67e+00
        pdb=" C   VAL J 199 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   VAL J 199 "    0.008 2.00e-02 2.50e+03
        pdb=" N   GLY J 200 "    0.007 2.00e-02 2.50e+03
  ... (remaining 903 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 675
        2.75 -     3.29: 5469
        3.29 -     3.82: 9989
        3.82 -     4.36: 11922
        4.36 -     4.90: 19406
  Nonbonded interactions: 47461
  Sorted by model distance:
  nonbonded pdb=" O   GLY H 286 "
            pdb=" O   HOH H 401 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   HOH J 501 "
            pdb=" O   HOH J 550 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   LEU I 236 "
            pdb=" O   HOH I 401 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   HOH J 555 "
            pdb=" O   HOH J 560 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   GLU I 145 "
            pdb=" O   HOH I 402 "
     model   vdw
     2.262 3.040
  ... (remaining 47456 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=0.49 max=1.00 mean=0.99
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:             4.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.660
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
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      :  0.005   0.110   5265  Z= 0.224
  Angle     :  0.628   9.294   7126  Z= 0.295
  Chirality :  0.042   0.186    781
  Planarity :  0.004   0.036    906
  Dihedral  : 16.385  87.437   1980
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.26 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 14.23 %
    Favored  : 85.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.71 (0.34), residues: 619
  helix:  1.92 (0.28), residues: 336
  sheet:  0.02 (1.52), residues: 18
  loop :  0.29 (0.38), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG I  21 
 TYR   0.016   0.002   TYR I  91 
 PHE   0.016   0.002   PHE I  30 
 TRP   0.010   0.001   TRP J 132 
 HIS   0.005   0.001   HIS J 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 5265)
  covalent geometry    : angle       0.62838 ( 7126)
  hydrogen bonds       : bond        0.14642 (  272)
  hydrogen bonds       : angle       6.28240 (  759)

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.163 
Fit side-chains
REVERT: H  259 HIS cc_start: 0.6931 (OUTLIER) cc_final: 0.6609 (t-90)
  outliers start: 4
  outliers final: 1
  residues processed: 100
  average time/residue: 0.6852
  time to fit residues: 70.7831
Evaluate side-chains
  92 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  259 HIS
Chi-restraints excluded: chain I residue  236 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0370
   chunk 56 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 61 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.4980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
H 281 GLN
I 142 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 130 GLN
J 258 HIS
J 259 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.189113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.157447 restraints weight = 21954.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3918 rms_B_bonded: 2.41
r_work: 0.3769 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3672 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3670
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3670 r_free = 0.3670    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3670 r_free = 0.3670    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3670
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.0671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   5265  Z= 0.122
  Angle     :  0.533   6.827   7126  Z= 0.271
  Chirality :  0.040   0.127    781
  Planarity :  0.004   0.037    906
  Dihedral  :  7.333  65.816    720
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.62 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.15 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  2.04 (0.34), residues: 619
  helix:  2.32 (0.28), residues: 334
  sheet: -0.74 (1.28), residues: 18
  loop :  0.33 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG J 309 
 TYR   0.017   0.002   TYR I  91 
 PHE   0.015   0.001   PHE I 110 
 TRP   0.007   0.001   TRP J 132 
 HIS   0.008   0.001   HIS J 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 5265)
  covalent geometry    : angle       0.53269 ( 7126)
  hydrogen bonds       : bond        0.04700 (  272)
  hydrogen bonds       : angle       4.88544 (  759)

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.208 
Fit side-chains
  outliers start: 9
  outliers final: 2
  residues processed: 102
  average time/residue: 0.6866
  time to fit residues: 72.4869
Evaluate side-chains
  91 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 89
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  134 LEU
Chi-restraints excluded: chain J residue  233 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
H 281 GLN
I 142 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.184886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.153839 restraints weight = 17639.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 2.14
r_work: 0.3739 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3643 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3642
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3642 r_free = 0.3642    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3642 r_free = 0.3642    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3642
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.1031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5265  Z= 0.233
  Angle     :  0.674   7.694   7126  Z= 0.343
  Chirality :  0.045   0.149    781
  Planarity :  0.005   0.034    906
  Dihedral  :  7.575  69.434    716
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.78 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 11.89 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.41 (0.33), residues: 619
  helix:  1.77 (0.28), residues: 333
  sheet: -1.21 (1.10), residues: 11
  loop :  0.07 (0.36), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG I  77 
 TYR   0.025   0.003   TYR I   2 
 PHE   0.017   0.003   PHE I 110 
 TRP   0.013   0.002   TRP J 132 
 HIS   0.008   0.002   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 5265)
  covalent geometry    : angle       0.67432 ( 7126)
  hydrogen bonds       : bond        0.05833 (  272)
  hydrogen bonds       : angle       5.21070 (  759)

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.235 
Fit side-chains
  outliers start: 13
  outliers final: 4
  residues processed: 107
  average time/residue: 0.6572
  time to fit residues: 72.6594
Evaluate side-chains
  95 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  259 HIS
Chi-restraints excluded: chain I residue  134 LEU
Chi-restraints excluded: chain J residue   25 THR
Chi-restraints excluded: chain J residue  233 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 34 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 27 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
I 142 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 130 GLN
J 172 GLN
J 258 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.187724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.156007 restraints weight = 20164.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3901 rms_B_bonded: 2.26
r_work: 0.3753 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3656 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3655
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3655 r_free = 0.3655    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3655 r_free = 0.3655    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3655
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.1023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5265  Z= 0.133
  Angle     :  0.550   7.355   7126  Z= 0.282
  Chirality :  0.041   0.133    781
  Planarity :  0.004   0.035    906
  Dihedral  :  7.283  68.115    716
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.78 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 12.97 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.68 (0.33), residues: 619
  helix:  2.02 (0.28), residues: 334
  sheet: -1.19 (1.05), residues: 11
  loop :  0.16 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I  21 
 TYR   0.018   0.002   TYR I  91 
 PHE   0.017   0.002   PHE I 110 
 TRP   0.010   0.001   TRP J 132 
 HIS   0.005   0.001   HIS J 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 5265)
  covalent geometry    : angle       0.55024 ( 7126)
  hydrogen bonds       : bond        0.04687 (  272)
  hydrogen bonds       : angle       4.84364 (  759)

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.219 
Fit side-chains
REVERT: I   18 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6716 (tp40)
  outliers start: 13
  outliers final: 4
  residues processed: 103
  average time/residue: 0.6456
  time to fit residues: 68.8677
Evaluate side-chains
  96 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  259 HIS
Chi-restraints excluded: chain I residue   18 GLN
Chi-restraints excluded: chain I residue  134 LEU
Chi-restraints excluded: chain J residue   25 THR
Chi-restraints excluded: chain J residue  233 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 26 optimal weight:    0.3980
   chunk 30 optimal weight:    2.9990
   chunk 4 optimal weight:    8.9990
   chunk 36 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 16 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 7 optimal weight:    0.0170
   chunk 27 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.4824

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

Flipped N/Q/H residues before XYZ refinement:
I 142 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 172 GLN
J 258 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.186019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.156243 restraints weight = 19149.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3911 rms_B_bonded: 2.35
r_work: 0.3733 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3638 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3637
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3637 r_free = 0.3637    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3637 r_free = 0.3637    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3637
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.1019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5265  Z= 0.182
  Angle     :  0.626   8.505   7126  Z= 0.318
  Chirality :  0.044   0.216    781
  Planarity :  0.005   0.036    906
  Dihedral  :  7.454  69.369    716
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.94 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 12.97 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.50 (0.33), residues: 619
  helix:  1.83 (0.28), residues: 334
  sheet: -0.85 (0.97), residues: 11
  loop :  0.10 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG I  77 
 TYR   0.022   0.002   TYR I   2 
 PHE   0.018   0.002   PHE I 110 
 TRP   0.012   0.002   TRP J 132 
 HIS   0.007   0.002   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 5265)
  covalent geometry    : angle       0.62562 ( 7126)
  hydrogen bonds       : bond        0.05252 (  272)
  hydrogen bonds       : angle       4.99425 (  759)

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.183 
Fit side-chains
REVERT: I   18 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6735 (tp40)
REVERT: I   28 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7264 (ppt170)
  outliers start: 13
  outliers final: 4
  residues processed: 101
  average time/residue: 0.6733
  time to fit residues: 70.3801
Evaluate side-chains
  95 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  259 HIS
Chi-restraints excluded: chain I residue   18 GLN
Chi-restraints excluded: chain I residue   28 ARG
Chi-restraints excluded: chain I residue  134 LEU
Chi-restraints excluded: chain J residue   25 THR
Chi-restraints excluded: chain J residue  233 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 46 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 58 optimal weight:    7.9990
   chunk 22 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
I 142 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 172 GLN
J 258 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.186112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.156287 restraints weight = 20211.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3912 rms_B_bonded: 2.35
r_work: 0.3744 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3647 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3646
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3646 r_free = 0.3646    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3646 r_free = 0.3646    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3646
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.1115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5265  Z= 0.169
  Angle     :  0.615   7.678   7126  Z= 0.311
  Chirality :  0.043   0.137    781
  Planarity :  0.005   0.037    906
  Dihedral  :  7.420  69.298    716
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.94 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.51 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.50 (0.33), residues: 619
  helix:  1.81 (0.28), residues: 334
  sheet: -0.59 (0.92), residues: 11
  loop :  0.12 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG I  21 
 TYR   0.021   0.002   TYR I   2 
 PHE   0.018   0.002   PHE I 110 
 TRP   0.011   0.002   TRP J 132 
 HIS   0.006   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 5265)
  covalent geometry    : angle       0.61500 ( 7126)
  hydrogen bonds       : bond        0.05086 (  272)
  hydrogen bonds       : angle       4.94096 (  759)

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.223 
Fit side-chains
REVERT: I   18 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6714 (tp40)
REVERT: I   28 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7268 (ppt170)
  outliers start: 11
  outliers final: 4
  residues processed: 99
  average time/residue: 0.7071
  time to fit residues: 72.5258
Evaluate side-chains
  95 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  259 HIS
Chi-restraints excluded: chain I residue   18 GLN
Chi-restraints excluded: chain I residue   28 ARG
Chi-restraints excluded: chain I residue  134 LEU
Chi-restraints excluded: chain J residue   25 THR
Chi-restraints excluded: chain J residue  233 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 3 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 56 optimal weight:    0.3980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
I 142 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 130 GLN
J 172 GLN
J 258 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.188181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.158385 restraints weight = 24371.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 2.81
r_work: 0.3752 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3656 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3654
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3654 r_free = 0.3654    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3654 r_free = 0.3654    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3654
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.1095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5265  Z= 0.127
  Angle     :  0.570   8.267   7126  Z= 0.289
  Chirality :  0.042   0.248    781
  Planarity :  0.004   0.036    906
  Dihedral  :  7.200  67.451    716
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.78 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 14.23 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.78 (0.33), residues: 619
  helix:  2.05 (0.28), residues: 334
  sheet: -0.60 (0.89), residues: 11
  loop :  0.25 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I  21 
 TYR   0.017   0.002   TYR I  91 
 PHE   0.018   0.002   PHE I 110 
 TRP   0.009   0.001   TRP J 132 
 HIS   0.006   0.001   HIS J 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 5265)
  covalent geometry    : angle       0.56957 ( 7126)
  hydrogen bonds       : bond        0.04447 (  272)
  hydrogen bonds       : angle       4.72772 (  759)

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: I   18 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6739 (tp40)
REVERT: I   28 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7239 (ppt170)
  outliers start: 9
  outliers final: 3
  residues processed: 102
  average time/residue: 0.6967
  time to fit residues: 73.5260
Evaluate side-chains
  93 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 88
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  259 HIS
Chi-restraints excluded: chain I residue   18 GLN
Chi-restraints excluded: chain I residue   28 ARG
Chi-restraints excluded: chain I residue  134 LEU
Chi-restraints excluded: chain J residue   25 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0870
   chunk 24 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0470
   chunk 19 optimal weight:    0.6980
   chunk 36 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0370
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.3134

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

Flipped N/Q/H residues before XYZ refinement:
I 142 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 130 GLN
J 172 GLN
J 258 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.190925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.159593 restraints weight = 24302.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 2.57
r_work: 0.3794 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3698 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3696
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3696 r_free = 0.3696    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3696 r_free = 0.3696    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3696
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.1330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   5265  Z= 0.105
  Angle     :  0.553   8.814   7126  Z= 0.277
  Chirality :  0.040   0.130    781
  Planarity :  0.004   0.038    906
  Dihedral  :  6.916  63.909    716
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.62 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 15.14 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  2.13 (0.33), residues: 619
  helix:  2.37 (0.28), residues: 335
  sheet: -0.82 (0.85), residues: 11
  loop :  0.37 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG I  21 
 TYR   0.015   0.001   TYR I  91 
 PHE   0.018   0.001   PHE I 110 
 TRP   0.010   0.001   TRP I  11 
 HIS   0.006   0.001   HIS J 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 5265)
  covalent geometry    : angle       0.55280 ( 7126)
  hydrogen bonds       : bond        0.03866 (  272)
  hydrogen bonds       : angle       4.49274 (  759)

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: H  259 HIS cc_start: 0.6928 (OUTLIER) cc_final: 0.6622 (t-90)
REVERT: I   21 ARG cc_start: 0.7610 (ttp-110) cc_final: 0.7218 (mtp-110)
  outliers start: 5
  outliers final: 2
  residues processed: 100
  average time/residue: 0.6866
  time to fit residues: 71.1265
Evaluate side-chains
  92 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  259 HIS
Chi-restraints excluded: chain I residue  134 LEU
Chi-restraints excluded: chain J residue   25 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0020
   chunk 6 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 50 optimal weight:    6.9990
   chunk 58 optimal weight:    6.9990
   chunk 31 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.9394

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

Flipped N/Q/H residues before XYZ refinement:
I 142 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 130 GLN
J 172 GLN
J 258 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.187966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.156634 restraints weight = 21862.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3910 rms_B_bonded: 2.39
r_work: 0.3754 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3658 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3657
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3657 r_free = 0.3657    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3657 r_free = 0.3657    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3657
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.1201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   5265  Z= 0.146
  Angle     :  0.627  11.636   7126  Z= 0.313
  Chirality :  0.042   0.136    781
  Planarity :  0.005   0.038    906
  Dihedral  :  7.195  67.517    716
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.94 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 15.50 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.90 (0.34), residues: 619
  helix:  2.09 (0.28), residues: 341
  sheet: -0.83 (0.83), residues: 11
  loop :  0.35 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I  21 
 TYR   0.019   0.002   TYR I   2 
 PHE   0.017   0.002   PHE I 110 
 TRP   0.009   0.001   TRP J 132 
 HIS   0.006   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 5265)
  covalent geometry    : angle       0.62712 ( 7126)
  hydrogen bonds       : bond        0.04589 (  272)
  hydrogen bonds       : angle       4.69975 (  759)

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
REVERT: H  259 HIS cc_start: 0.6896 (OUTLIER) cc_final: 0.6597 (t-90)
REVERT: I   28 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7208 (ppt170)
  outliers start: 7
  outliers final: 3
  residues processed: 92
  average time/residue: 0.7054
  time to fit residues: 67.1807
Evaluate side-chains
  92 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  259 HIS
Chi-restraints excluded: chain I residue   28 ARG
Chi-restraints excluded: chain I residue  134 LEU
Chi-restraints excluded: chain J residue   25 THR
Chi-restraints excluded: chain J residue  233 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0470
   chunk 22 optimal weight:    0.8980
   chunk 4 optimal weight:   10.0000
   chunk 39 optimal weight:    8.9990
   chunk 54 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0980
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
I 142 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 130 GLN
J 172 GLN
J 258 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.189960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.158747 restraints weight = 23581.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3936 rms_B_bonded: 2.48
r_work: 0.3767 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3671 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3668
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3668 r_free = 0.3668    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3668 r_free = 0.3668    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3668
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.1335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   5265  Z= 0.121
  Angle     :  0.609  11.317   7126  Z= 0.305
  Chirality :  0.041   0.140    781
  Planarity :  0.004   0.039    906
  Dihedral  :  7.049  65.814    716
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.62 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 15.68 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  2.01 (0.34), residues: 619
  helix:  2.19 (0.28), residues: 341
  sheet: -0.97 (0.84), residues: 11
  loop :  0.39 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I  21 
 TYR   0.015   0.001   TYR I  91 
 PHE   0.018   0.001   PHE I 110 
 TRP   0.008   0.001   TRP I  11 
 HIS   0.006   0.001   HIS J 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 5265)
  covalent geometry    : angle       0.60884 ( 7126)
  hydrogen bonds       : bond        0.04111 (  272)
  hydrogen bonds       : angle       4.55214 (  759)

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

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

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1238 Ramachandran restraints generated.
    619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: H  259 HIS cc_start: 0.6941 (OUTLIER) cc_final: 0.6643 (t-90)
REVERT: I   28 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7124 (ppt170)
  outliers start: 6
  outliers final: 2
  residues processed: 95
  average time/residue: 0.7182
  time to fit residues: 70.5841
Evaluate side-chains
  92 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  259 HIS
Chi-restraints excluded: chain I residue   28 ARG
Chi-restraints excluded: chain I residue  134 LEU
Chi-restraints excluded: chain J residue   25 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0010
   chunk 33 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 48 optimal weight:    0.3980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.8188

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

Flipped N/Q/H residues before XYZ refinement:
I 142 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 130 GLN
J 172 GLN
J 258 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.188568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.159331 restraints weight = 18989.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 2.28
r_work: 0.3777 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3680 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3678
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3678 r_free = 0.3678    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3678 r_free = 0.3678    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3678
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.1232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   5265  Z= 0.140
  Angle     :  0.641  12.057   7126  Z= 0.320
  Chirality :  0.042   0.147    781
  Planarity :  0.005   0.045    906
  Dihedral  :  7.192  67.256    716
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.10 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 15.32 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  1.90 (0.33), residues: 619
  helix:  2.09 (0.28), residues: 341
  sheet: -0.90 (0.82), residues: 11
  loop :  0.36 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG I  21 
 TYR   0.018   0.002   TYR I   2 
 PHE   0.017   0.002   PHE I 110 
 TRP   0.009   0.001   TRP J 132 
 HIS   0.006   0.001   HIS J 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 5265)
  covalent geometry    : angle       0.64104 ( 7126)
  hydrogen bonds       : bond        0.04464 (  272)
  hydrogen bonds       : angle       4.66337 (  759)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3591.94 seconds
wall clock time: 61 minutes 45.27 seconds (3705.27 seconds total)