Starting phenix.real_space_refine
on Thu Mar  6 06:58:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p77_17520/03_2025/8p77_17520.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p77_17520/03_2025/8p77_17520.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=1.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p77_17520/03_2025/8p77_17520.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p77_17520/03_2025/8p77_17520.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p77_17520/03_2025/8p77_17520.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p77_17520/03_2025/8p77_17520.cif"
  }
  resolution = 1.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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    3313      2.51       5
     N     876      2.21       5
     O    1051      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5271
  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: 2283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2283
          Classifications: {'peptide': 286}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267}
          Chain breaks: 2
    Chain: "J"
      Number of atoms: 58
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1, 29
          Unusual residues: {'I73': 1}
          Classifications: {'undetermined': 1}
      Conformer: "B"
        Number of residues, atoms: 1, 29
          Unusual residues: {'I73': 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: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 58
          Classifications: {'water': 58}
          Link IDs: {None: 57}
    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=" C11AI73 J 401 " occ=0.50
      ... (56 atoms not shown)
      pdb=" O1 BI73 J 401 " occ=0.50
  Time building chain proxies: 5.48, per 1000 atoms: 1.04
  Number of scatterers: 5271
  At special positions: 0
  Unit cell: (84.7875, 93.3375, 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    1051      8.00
     N     876      7.00
     C    3313      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: 1.55
  Conformation dependent library (CDL) restraints added in 603.9 milliseconds
  

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1196

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 3 sheets defined
      61.9% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'H' and resid 270 through 275
      removed outlier: 3.513A  pdb=" N   ASN H 273 " --> pdb=" O   GLY H 270 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   VAL H 275 " --> pdb=" O   LEU H 272 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 279 through 286
    Processing helix  chain 'H' and resid 288 through 302
      removed outlier: 3.796A  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: 3.908A  pdb=" N   ASN I  93 " --> pdb=" O   ARG I  89 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 100 through 116
      removed outlier: 3.669A  pdb=" N   LEU I 106 " --> pdb=" O   ARG I 102 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 121 through 128
      removed outlier: 3.687A  pdb=" N   ASN I 128 " --> pdb=" O   GLN I 124 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 132 through 154
      removed outlier: 4.805A  pdb=" N   LEU I 148 " --> pdb=" O   LEU I 144 " (cutoff:3.500A)
      removed outlier: 4.575A  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
    Processing helix  chain 'I' and resid 187 through 201
      removed outlier: 3.738A  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 225
    Processing helix  chain 'I' and resid 228 through 234
      removed outlier: 3.631A  pdb=" N   LEU I 232 " --> pdb=" O   MET I 228 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 241 through 262
    Processing helix  chain 'I' and resid 266 through 283
    Processing helix  chain 'J' and resid 56 through 67
    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: 4.298A  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: 3.851A  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
    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 291
    Processing helix  chain 'J' and resid 292 through 297
      removed outlier: 3.738A  pdb=" N   SER J 296 " --> pdb=" O   MET J 292 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 303 through 307
    Processing sheet with id=AA1, first strand: chain 'J' and resid 13 through 20
      removed outlier: 7.333A  pdb=" N   LEU J  15 " --> pdb=" O   ARG J  30 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   ARG J  30 " --> pdb=" O   LEU J  15 " (cutoff:3.500A)
      removed outlier: 5.458A  pdb=" N   PHE J  17 " --> pdb=" O   LYS J  28 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   LYS J  28 " --> pdb=" O   PHE J  17 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASP J  79 " --> pdb=" O   VAL J  90 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   ASP J  92 " --> pdb=" O   LEU J  77 " (cutoff:3.500A)
      removed outlier: 8.007A  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

    273 hydrogen bonds defined for protein.
    768 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.53

  Time building geometry restraints manager: 1.72 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: 1642
        1.34 -     1.46: 1170
        1.46 -     1.58: 2398
        1.58 -     1.69: 2
        1.69 -     1.81: 49
  Bond restraints: 5261
  Sorted by residual:
  bond pdb=" C3 AI73 J 401 "
       pdb=" N10AI73 J 401 "
    ideal  model  delta    sigma   weight residual
    1.339  1.517 -0.178 2.00e-02 2.50e+03 7.90e+01
  bond pdb=" C3 BI73 J 401 "
       pdb=" N10BI73 J 401 "
    ideal  model  delta    sigma   weight residual
    1.339  1.516 -0.177 2.00e-02 2.50e+03 7.83e+01
  bond pdb=" C5 BI73 J 401 "
       pdb=" N18BI73 J 401 "
    ideal  model  delta    sigma   weight residual
    1.349  1.480 -0.131 2.00e-02 2.50e+03 4.32e+01
  bond pdb=" C5 AI73 J 401 "
       pdb=" N18AI73 J 401 "
    ideal  model  delta    sigma   weight residual
    1.349  1.480 -0.131 2.00e-02 2.50e+03 4.29e+01
  bond pdb=" N1 AI73 J 401 "
       pdb=" N2 AI73 J 401 "
    ideal  model  delta    sigma   weight residual
    1.343  1.415 -0.072 2.00e-02 2.50e+03 1.29e+01
  ... (remaining 5256 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 6926
        1.45 -     2.89: 140
        2.89 -     4.34: 44
        4.34 -     5.78: 4
        5.78 -     7.23: 7
  Bond angle restraints: 7121
  Sorted by residual:
  angle pdb=" C4 BI73 J 401 "
        pdb=" C3 BI73 J 401 "
        pdb=" N10BI73 J 401 "
      ideal   model   delta    sigma   weight residual
     127.16  119.93    7.23 3.00e+00 1.11e-01 5.81e+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  109.65    4.25 1.80e+00 3.09e-01 5.58e+00
  angle pdb=" C4 AI73 J 401 "
        pdb=" C3 AI73 J 401 "
        pdb=" N10AI73 J 401 "
      ideal   model   delta    sigma   weight residual
     127.16  120.17    6.99 3.00e+00 1.11e-01 5.44e+00
  angle pdb=" CB  MET J 189 "
        pdb=" CG  MET J 189 "
        pdb=" SD  MET J 189 "
      ideal   model   delta    sigma   weight residual
     112.70  119.39   -6.69 3.00e+00 1.11e-01 4.97e+00
  angle pdb=" C8 BI73 J 401 "
        pdb=" C9 BI73 J 401 "
        pdb=" N1 BI73 J 401 "
      ideal   model   delta    sigma   weight residual
     113.59  107.37    6.22 3.00e+00 1.11e-01 4.30e+00
  ... (remaining 7116 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.84: 2806
       18.84 -    37.68: 287
       37.68 -    56.51: 63
       56.51 -    75.35: 19
       75.35 -    94.19: 6
  Dihedral angle restraints: 3181
    sinusoidal: 1334
      harmonic: 1847
  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  162.41   17.59     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" C41AI73 J 401 "
           pdb=" C40AI73 J 401 "
           pdb=" N18AI73 J 401 "
           pdb=" C5 AI73 J 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     166.20  -99.61  -94.19     1      3.00e+01 1.11e-03 1.14e+01
  dihedral pdb=" CB  GLU J  99 "
           pdb=" CG  GLU J  99 "
           pdb=" CD  GLU J  99 "
           pdb=" OE1 GLU J  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.27   88.27     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 3178 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 495
       0.028 -    0.057: 170
       0.057 -    0.085: 72
       0.085 -    0.114: 36
       0.114 -    0.142: 6
  Chirality restraints: 779
  Sorted by residual:
  chirality pdb=" CA  TYR I  91 "
            pdb=" N   TYR I  91 "
            pdb=" C   TYR I  91 "
            pdb=" CB  TYR I  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.06e-01
  chirality pdb=" CA  ILE J  74 "
            pdb=" N   ILE J  74 "
            pdb=" C   ILE J  74 "
            pdb=" CB  ILE J  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.15e-01
  chirality pdb=" CA  VAL J 210 "
            pdb=" N   VAL J 210 "
            pdb=" C   VAL J 210 "
            pdb=" CB  VAL J 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.78e-01
  ... (remaining 776 not shown)

  Planarity restraints: 905
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS J 139 "    0.023 5.00e-02 4.00e+02   3.47e-02 1.93e+00
        pdb=" N   PRO J 140 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO J 140 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO J 140 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP I 193 "    0.006 2.00e-02 2.50e+03   1.27e-02 1.60e+00
        pdb=" C   ASP I 193 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   ASP I 193 "    0.008 2.00e-02 2.50e+03
        pdb=" N   PHE I 194 "    0.007 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   1.19e-02 1.42e+00
        pdb=" C   VAL J 199 "   -0.021 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 902 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 973
        2.76 -     3.30: 5275
        3.30 -     3.83: 10028
        3.83 -     4.37: 11749
        4.37 -     4.90: 19327
  Nonbonded interactions: 47352
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP J  97 "
            pdb=" O   HOH J 501 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   HOH J 514 "
            pdb=" O   HOH J 552 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   PHE J 295 "
            pdb=" O   HOH J 502 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   HOH I 403 "
            pdb=" O   HOH I 445 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   GLU I 145 "
            pdb=" O   HOH I 401 "
     model   vdw
     2.277 3.040
  ... (remaining 47347 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=0.50 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:             65.050
  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:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.690
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:20.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  104.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.178   5261  Z= 0.406
  Angle     :  0.583   7.229   7121  Z= 0.275
  Chirality :  0.039   0.142    779
  Planarity :  0.004   0.035    905
  Dihedral  : 16.680  94.189   1985
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 14.98 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.34), residues: 618
  helix:  2.07 (0.29), residues: 339
  sheet:  1.40 (1.58), residues: 10
  loop :  0.48 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP I  11 
 HIS   0.003   0.001   HIS I 161 
 PHE   0.014   0.002   PHE I 110 
 TYR   0.016   0.002   TYR I  60 
 ARG   0.007   0.001   ARG H 268 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 0.640 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 106
  average time/residue: 1.5165
  time to fit residues: 167.1236
Evaluate side-chains
  106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  290 SER
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  132 SER
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain J residue  106 SER
Chi-restraints excluded: chain J residue  302 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0970
   chunk 36 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
I 124 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 130 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.173096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.146111 restraints weight = 17296.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3813 rms_B_bonded: 2.03
r_work: 0.3694 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3610 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3609
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3609 r_free = 0.3609    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3609 r_free = 0.3609    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3609
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.0681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5261  Z= 0.187
  Angle     :  0.544   6.042   7121  Z= 0.281
  Chirality :  0.041   0.138    779
  Planarity :  0.005   0.033    905
  Dihedral  :  8.173  93.519    730
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 14.26 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.34), residues: 618
  helix:  2.06 (0.29), residues: 345
  sheet:  2.23 (1.26), residues: 15
  loop :  0.40 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP I  11 
 HIS   0.004   0.001   HIS I 161 
 PHE   0.014   0.002   PHE J  91 
 TYR   0.021   0.002   TYR I  91 
 ARG   0.004   0.001   ARG H 268 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.580 
Fit side-chains
REVERT: J   92 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7361 (m-30)
  outliers start: 7
  outliers final: 3
  residues processed: 106
  average time/residue: 1.3931
  time to fit residues: 153.1229
Evaluate side-chains
  104 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  229 GLU
Chi-restraints excluded: chain J residue   53 ASP
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  302 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 39 optimal weight:    8.9990
   chunk 3 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0040
   overall best weight:    0.8796

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.173080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.146419 restraints weight = 15742.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3820 rms_B_bonded: 1.94
r_work: 0.3704 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3621 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3620
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3620 r_free = 0.3620    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3620 r_free = 0.3620    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3620
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.0777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5261  Z= 0.174
  Angle     :  0.523   5.897   7121  Z= 0.270
  Chirality :  0.040   0.141    779
  Planarity :  0.004   0.034    905
  Dihedral  :  7.635  92.722    724
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 13.72 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.34), residues: 618
  helix:  2.17 (0.28), residues: 340
  sheet:  2.48 (1.30), residues: 15
  loop :  0.56 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP I  11 
 HIS   0.004   0.001   HIS I 161 
 PHE   0.013   0.002   PHE J 295 
 TYR   0.020   0.002   TYR I  91 
 ARG   0.005   0.001   ARG I  28 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.632 
Fit side-chains
REVERT: J   42 LYS cc_start: 0.5874 (OUTLIER) cc_final: 0.5162 (mmmt)
REVERT: J   92 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7348 (m-30)
  outliers start: 13
  outliers final: 7
  residues processed: 111
  average time/residue: 1.4286
  time to fit residues: 164.5018
Evaluate side-chains
  107 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  229 GLU
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   53 ASP
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  106 SER
Chi-restraints excluded: chain J residue  169 TYR
Chi-restraints excluded: chain J residue  302 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 25 optimal weight:    0.3980
   chunk 34 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 29 optimal weight:    0.4980
   chunk 35 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 130 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.174211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.147511 restraints weight = 18364.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3833 rms_B_bonded: 2.06
r_work: 0.3709 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3624 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3622
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3622 r_free = 0.3622    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3622 r_free = 0.3622    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3622
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.0820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5261  Z= 0.158
  Angle     :  0.503   5.825   7121  Z= 0.261
  Chirality :  0.040   0.138    779
  Planarity :  0.004   0.034    905
  Dihedral  :  7.481  92.367    724
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.46 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.08 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.34), residues: 618
  helix:  2.21 (0.28), residues: 340
  sheet:  2.71 (1.30), residues: 15
  loop :  0.62 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP I  11 
 HIS   0.003   0.001   HIS I 161 
 PHE   0.013   0.002   PHE J  81 
 TYR   0.019   0.002   TYR I  91 
 ARG   0.005   0.001   ARG H 268 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.603 
Fit side-chains
REVERT: I  189 LYS cc_start: 0.7541 (ttpp) cc_final: 0.7323 (tptp)
REVERT: J   42 LYS cc_start: 0.5850 (OUTLIER) cc_final: 0.5125 (mmmt)
REVERT: J   92 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7340 (m-30)
  outliers start: 11
  outliers final: 6
  residues processed: 110
  average time/residue: 1.3593
  time to fit residues: 155.1223
Evaluate side-chains
  108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  132 SER
Chi-restraints excluded: chain I residue  229 GLU
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  106 SER
Chi-restraints excluded: chain J residue  169 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 5 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
I 155 ASN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.172962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.146537 restraints weight = 15174.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3817 rms_B_bonded: 1.85
r_work: 0.3704 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3620 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3620
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3620 r_free = 0.3620    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3620 r_free = 0.3620    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3620
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.0841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5261  Z= 0.192
  Angle     :  0.540   6.065   7121  Z= 0.279
  Chirality :  0.041   0.142    779
  Planarity :  0.005   0.034    905
  Dihedral  :  7.444  91.627    723
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.46 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 14.44 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.34), residues: 618
  helix:  2.12 (0.28), residues: 340
  sheet:  2.61 (1.31), residues: 15
  loop :  0.60 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP I  11 
 HIS   0.004   0.001   HIS J 131 
 PHE   0.013   0.002   PHE J 295 
 TYR   0.021   0.002   TYR I  91 
 ARG   0.005   0.001   ARG H 268 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.655 
Fit side-chains
REVERT: I  189 LYS cc_start: 0.7564 (ttpp) cc_final: 0.7353 (tptp)
REVERT: J   42 LYS cc_start: 0.5879 (OUTLIER) cc_final: 0.5113 (mmmt)
REVERT: J   92 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7357 (m-30)
  outliers start: 14
  outliers final: 7
  residues processed: 114
  average time/residue: 1.4759
  time to fit residues: 174.3481
Evaluate side-chains
  109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  132 SER
Chi-restraints excluded: chain I residue  229 GLU
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  106 SER
Chi-restraints excluded: chain J residue  169 TYR
Chi-restraints excluded: chain J residue  302 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 6 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 39 optimal weight:    6.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
I 155 ASN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.172621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.145673 restraints weight = 18379.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3810 rms_B_bonded: 2.06
r_work: 0.3691 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3605 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3605
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3605 r_free = 0.3605    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3605 r_free = 0.3605    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3605
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.0899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5261  Z= 0.195
  Angle     :  0.543   6.027   7121  Z= 0.281
  Chirality :  0.041   0.144    779
  Planarity :  0.005   0.033    905
  Dihedral  :  7.416  90.941    723
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.46 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.62 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.34), residues: 618
  helix:  2.08 (0.28), residues: 340
  sheet:  2.57 (1.32), residues: 15
  loop :  0.60 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP I  11 
 HIS   0.004   0.001   HIS J 131 
 PHE   0.014   0.002   PHE J  81 
 TYR   0.021   0.002   TYR I  91 
 ARG   0.005   0.001   ARG H 268 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.610 
Fit side-chains
REVERT: J   42 LYS cc_start: 0.5895 (OUTLIER) cc_final: 0.5162 (mmmt)
REVERT: J   92 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7408 (m-30)
  outliers start: 12
  outliers final: 8
  residues processed: 110
  average time/residue: 1.4601
  time to fit residues: 166.7125
Evaluate side-chains
  111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  132 SER
Chi-restraints excluded: chain I residue  229 GLU
Chi-restraints excluded: chain J residue   16 ASP
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   53 ASP
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  106 SER
Chi-restraints excluded: chain J residue  169 TYR
Chi-restraints excluded: chain J residue  302 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
I 155 ASN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.172215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.143934 restraints weight = 26842.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 2.51
r_work: 0.3661 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3576 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3576
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3576
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.0922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5261  Z= 0.220
  Angle     :  0.570   6.106   7121  Z= 0.294
  Chirality :  0.042   0.145    779
  Planarity :  0.005   0.038    905
  Dihedral  :  7.452  90.108    723
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.62 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 14.80 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.34), residues: 618
  helix:  1.98 (0.28), residues: 340
  sheet:  2.54 (1.31), residues: 15
  loop :  0.58 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP I  11 
 HIS   0.005   0.001   HIS I 281 
 PHE   0.013   0.002   PHE J 295 
 TYR   0.022   0.002   TYR I  91 
 ARG   0.006   0.001   ARG H 268 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.717 
Fit side-chains
REVERT: I  268 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.5918 (pm20)
REVERT: J   42 LYS cc_start: 0.5902 (OUTLIER) cc_final: 0.5195 (mmmt)
REVERT: J   92 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7525 (m-30)
  outliers start: 13
  outliers final: 8
  residues processed: 112
  average time/residue: 1.4197
  time to fit residues: 165.1239
Evaluate side-chains
  113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  132 SER
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain I residue  229 GLU
Chi-restraints excluded: chain I residue  268 GLU
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   53 ASP
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  106 SER
Chi-restraints excluded: chain J residue  169 TYR
Chi-restraints excluded: chain J residue  302 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 3 optimal weight:    0.4980
   chunk 13 optimal weight:    7.9990
   chunk 14 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
I 155 ASN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.171512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.144234 restraints weight = 19599.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3792 rms_B_bonded: 2.15
r_work: 0.3669 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3585 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3583
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3583 r_free = 0.3583    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3583 r_free = 0.3583    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3583
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.0928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5261  Z= 0.230
  Angle     :  0.586   6.117   7121  Z= 0.302
  Chirality :  0.042   0.146    779
  Planarity :  0.005   0.035    905
  Dihedral  :  7.478  89.630    723
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.62 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.34 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.34), residues: 618
  helix:  1.89 (0.28), residues: 340
  sheet:  2.56 (1.31), residues: 15
  loop :  0.54 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP I  11 
 HIS   0.005   0.001   HIS I 281 
 PHE   0.014   0.002   PHE I  71 
 TYR   0.022   0.002   TYR I  91 
 ARG   0.006   0.001   ARG I  77 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.617 
Fit side-chains
REVERT: I  268 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5827 (pm20)
REVERT: J   42 LYS cc_start: 0.5906 (OUTLIER) cc_final: 0.5108 (mmmt)
REVERT: J   92 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7459 (m-30)
  outliers start: 12
  outliers final: 8
  residues processed: 108
  average time/residue: 1.4049
  time to fit residues: 157.5780
Evaluate side-chains
  113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  132 SER
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain I residue  229 GLU
Chi-restraints excluded: chain I residue  268 GLU
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   53 ASP
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  106 SER
Chi-restraints excluded: chain J residue  169 TYR
Chi-restraints excluded: chain J residue  302 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 16 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
I 155 ASN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.173065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.144954 restraints weight = 23838.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3799 rms_B_bonded: 2.41
r_work: 0.3672 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3591 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3589
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.0916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5261  Z= 0.174
  Angle     :  0.541   5.883   7121  Z= 0.277
  Chirality :  0.041   0.143    779
  Planarity :  0.005   0.055    905
  Dihedral  :  7.332  89.563    723
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 15.52 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.34), residues: 618
  helix:  2.08 (0.28), residues: 340
  sheet:  2.80 (1.36), residues: 15
  loop :  0.59 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP I  11 
 HIS   0.004   0.001   HIS I 161 
 PHE   0.013   0.002   PHE J 295 
 TYR   0.019   0.002   TYR I  91 
 ARG   0.007   0.001   ARG H 268 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.611 
Fit side-chains
REVERT: I  189 LYS cc_start: 0.7666 (ttpp) cc_final: 0.7394 (tptp)
REVERT: I  268 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5832 (pm20)
REVERT: J   42 LYS cc_start: 0.5915 (OUTLIER) cc_final: 0.5165 (mmmt)
REVERT: J   92 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7452 (m-30)
  outliers start: 11
  outliers final: 7
  residues processed: 109
  average time/residue: 1.3591
  time to fit residues: 153.8233
Evaluate side-chains
  112 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  132 SER
Chi-restraints excluded: chain I residue  200 LEU
Chi-restraints excluded: chain I residue  229 GLU
Chi-restraints excluded: chain I residue  268 GLU
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   92 ASP
Chi-restraints excluded: chain J residue  106 SER
Chi-restraints excluded: chain J residue  169 TYR
Chi-restraints excluded: chain J residue  302 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 45 optimal weight:    8.9990
   chunk 42 optimal weight:    0.0370
   chunk 28 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0470
   chunk 23 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0470
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.3654

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
I 155 ASN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.175853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.149132 restraints weight = 21267.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 2.30
r_work: 0.3720 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3640 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3639
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
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      :  0.002   0.027   5261  Z= 0.142
  Angle     :  0.507   6.813   7121  Z= 0.258
  Chirality :  0.039   0.142    779
  Planarity :  0.004   0.035    905
  Dihedral  :  7.098  89.674    723
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.62 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 16.25 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.37 (0.35), residues: 618
  helix:  2.28 (0.28), residues: 340
  sheet:  2.73 (1.34), residues: 15
  loop :  0.67 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP J 197 
 HIS   0.003   0.001   HIS I 161 
 PHE   0.016   0.001   PHE J  81 
 TYR   0.016   0.002   TYR I  60 
 ARG   0.008   0.001   ARG I  77 

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.638 
Fit side-chains
REVERT: I   63 ARG cc_start: 0.7647 (mmm-85) cc_final: 0.7340 (mmm160)
REVERT: I  189 LYS cc_start: 0.7632 (ttpp) cc_final: 0.7382 (tptp)
REVERT: J   42 LYS cc_start: 0.5824 (OUTLIER) cc_final: 0.5036 (mmmt)
REVERT: J   92 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7259 (m-30)
  outliers start: 8
  outliers final: 2
  residues processed: 108
  average time/residue: 1.4163
  time to fit residues: 158.8234
Evaluate side-chains
  105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  132 SER
Chi-restraints excluded: chain I residue  229 GLU
Chi-restraints excluded: chain J residue   42 LYS
Chi-restraints excluded: chain J residue   92 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 25 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
H 249 GLN
I  18 GLN
I 155 ASN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.172982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.145779 restraints weight = 18549.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 2.09
r_work: 0.3688 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3604 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3601
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3601 r_free = 0.3601    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3601 r_free = 0.3601    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3601
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.0981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5261  Z= 0.200
  Angle     :  0.572   6.807   7121  Z= 0.292
  Chirality :  0.041   0.144    779
  Planarity :  0.005   0.034    905
  Dihedral  :  7.224  89.565    723
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.62 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 16.25 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.34), residues: 618
  helix:  2.13 (0.28), residues: 340
  sheet:  2.67 (1.33), residues: 15
  loop :  0.61 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP I  11 
 HIS   0.004   0.001   HIS I 281 
 PHE   0.013   0.002   PHE J  91 
 TYR   0.020   0.002   TYR I  91 
 ARG   0.006   0.001   ARG H 268 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7774.47 seconds
wall clock time: 133 minutes 28.63 seconds (8008.63 seconds total)