Starting phenix.real_space_refine
on Tue Feb 11 10:21:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p77_17520/02_2025/8p77_17520.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p77_17520/02_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_17520/02_2025/8p77_17520.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p77_17520/02_2025/8p77_17520.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p77_17520/02_2025/8p77_17520.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p77_17520/02_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.46, per 1000 atoms: 0.85
  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: 1.21
  Conformation dependent library (CDL) restraints added in 572.0 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: 0.56
  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: 1.56

  Time building geometry restraints manager: 1.40 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:             3.670
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     17.040
  Find NCS groups from input model:        0.080
  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:13.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.570
-------------------------------------------------------------------------------
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  : 0.670 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 106
  average time/residue: 1.4529
  time to fit residues: 159.7629
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  : 0.652 
-------------------------------------------------------------------------------
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:    0.6980
   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:    0.9380

-------------------------------------------------------------------------------
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 = 0.4146 r_free = 0.4146 target = 0.173217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.146344 restraints weight = 17075.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 2.00
r_work: 0.3697 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3612 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3611
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3611 r_free = 0.3611    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 = 0.3611 r_free = 0.3611    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3611
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.0661

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= 0.183
  Angle     :  0.540   5.987   7121  Z= 0.279
  Chirality :  0.041   0.138    779
  Planarity :  0.005   0.033    905
  Dihedral  :  8.170  93.722    730
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.37
  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:  2.04 (0.34), residues: 618
  helix:  2.07 (0.29), residues: 345
  sheet:  2.22 (1.26), residues: 15
  loop :  0.41 (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 J 131 
 PHE   0.014   0.002   PHE J 295 
 TYR   0.020   0.002   TYR I  91 
 ARG   0.004   0.000   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
  110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.665 
Fit side-chains
REVERT: J   92 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7354 (m-30)
  outliers start: 7
  outliers final: 3
  residues processed: 106
  average time/residue: 1.4522
  time to fit residues: 159.7202
Evaluate side-chains
  103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 43 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 39 optimal weight:    8.9990
   chunk 3 optimal weight:    4.9990
   chunk 25 optimal weight:    0.1980
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4134 r_free = 0.4134 target = 0.172367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.145648 restraints weight = 15814.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3810 rms_B_bonded: 1.94
r_work: 0.3692 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3607 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3607
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3607 r_free = 0.3607    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3607 r_free = 0.3607    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3607
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.0795

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= 0.196
  Angle     :  0.547   6.038   7121  Z= 0.283
  Chirality :  0.041   0.143    779
  Planarity :  0.005   0.034    905
  Dihedral  :  7.722  92.566    724
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 13.90 %
    Favored  : 83.75 %
  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:  1.93 (0.34), residues: 618
  helix:  1.97 (0.28), residues: 345
  sheet:  2.44 (1.29), residues: 15
  loop :  0.35 (0.39), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP I  11 
 HIS   0.004   0.001   HIS I 281 
 PHE   0.014   0.002   PHE J 295 
 TYR   0.021   0.002   TYR I  91 
 ARG   0.004   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  : 0.526 
Fit side-chains
REVERT: J   42 LYS cc_start: 0.5891 (OUTLIER) cc_final: 0.5168 (mmmt)
REVERT: J   92 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7403 (m-30)
  outliers start: 13
  outliers final: 6
  residues processed: 111
  average time/residue: 1.4584
  time to fit residues: 167.6812
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  : 0.657 
-------------------------------------------------------------------------------
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  302 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 25 optimal weight:    0.2980
   chunk 34 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 29 optimal weight:    0.4980
   chunk 35 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.6182

-------------------------------------------------------------------------------
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 = 0.4157 r_free = 0.4157 target = 0.174229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.147099 restraints weight = 18464.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3825 rms_B_bonded: 2.12
r_work: 0.3703 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3620 rms_B_bonded: 3.93 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 = 0.34   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: 0.7833
moved from start:          0.0810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5261  Z= 0.152
  Angle     :  0.500   5.829   7121  Z= 0.259
  Chirality :  0.040   0.139    779
  Planarity :  0.004   0.034    905
  Dihedral  :  7.503  92.178    724
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.46 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 14.62 %
    Favored  : 83.57 %
  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:  2.26 (0.34), residues: 618
  helix:  2.20 (0.28), residues: 340
  sheet:  2.66 (1.31), residues: 15
  loop :  0.60 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP I  11 
 HIS   0.003   0.001   HIS I 161 
 PHE   0.013   0.002   PHE J  81 
 TYR   0.018   0.002   TYR I  91 
 ARG   0.006   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
  118 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.578 
Fit side-chains
REVERT: I  189 LYS cc_start: 0.7537 (ttpp) cc_final: 0.7310 (tptp)
REVERT: J   42 LYS cc_start: 0.5850 (OUTLIER) cc_final: 0.5124 (mmmt)
REVERT: J   92 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7346 (m-30)
  outliers start: 10
  outliers final: 5
  residues processed: 111
  average time/residue: 1.5124
  time to fit residues: 173.7915
Evaluate side-chains
  108 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
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  169 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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**
J 130 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.173431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.146951 restraints weight = 14931.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3823 rms_B_bonded: 1.87
r_work: 0.3708 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3623 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3622
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3622 r_free = 0.3622    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3622 r_free = 0.3622    target_work(ls_wunit_k1) = 0.130         |
| 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: 0.7836
moved from start:          0.0839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5261  Z= 0.178
  Angle     :  0.528   6.005   7121  Z= 0.273
  Chirality :  0.040   0.141    779
  Planarity :  0.004   0.034    905
  Dihedral  :  7.428  91.808    723
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.44 %
    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:  2.22 (0.34), residues: 618
  helix:  2.16 (0.28), residues: 340
  sheet:  2.62 (1.31), residues: 15
  loop :  0.60 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J 131 
 PHE   0.013   0.002   PHE J 295 
 TYR   0.020   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: 15
    poor density    : 104
  time to evaluate  : 0.593 
Fit side-chains
REVERT: I  189 LYS cc_start: 0.7574 (ttpp) cc_final: 0.7355 (tptp)
REVERT: J   42 LYS cc_start: 0.5884 (OUTLIER) cc_final: 0.5153 (mmmt)
REVERT: J   92 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7357 (m-30)
  outliers start: 15
  outliers final: 7
  residues processed: 112
  average time/residue: 1.4323
  time to fit residues: 166.2689
Evaluate side-chains
  111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 18 optimal weight:    0.2980
   chunk 6 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 39 optimal weight:    6.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4156 r_free = 0.4156 target = 0.174165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.147352 restraints weight = 17274.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3829 rms_B_bonded: 1.99
r_work: 0.3712 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3628 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3627
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3627
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
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= 0.161
  Angle     :  0.510   5.862   7121  Z= 0.263
  Chirality :  0.040   0.139    779
  Planarity :  0.004   0.034    905
  Dihedral  :  7.312  91.423    723
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.46 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.98 %
    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:  2.28 (0.34), residues: 618
  helix:  2.21 (0.28), residues: 340
  sheet:  2.59 (1.31), residues: 15
  loop :  0.63 (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   0.014   0.002   PHE J  81 
 TYR   0.019   0.002   TYR I  91 
 ARG   0.006   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
  116 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.747 
Fit side-chains
REVERT: J   42 LYS cc_start: 0.5829 (OUTLIER) cc_final: 0.5093 (mmmt)
REVERT: J   92 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7326 (m-30)
  outliers start: 12
  outliers final: 8
  residues processed: 111
  average time/residue: 1.4449
  time to fit residues: 166.3329
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  : 0.624 
-------------------------------------------------------------------------------
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 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 29 optimal weight:    0.4980
   chunk 9 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.4145 r_free = 0.4145 target = 0.173184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.145868 restraints weight = 25856.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3812 rms_B_bonded: 2.36
r_work: 0.3676 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3592 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3591
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3591 r_free = 0.3591    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3591 r_free = 0.3591    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3591
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.0907

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= 0.188
  Angle     :  0.539   5.956   7121  Z= 0.277
  Chirality :  0.041   0.141    779
  Planarity :  0.004   0.034    905
  Dihedral  :  7.324  91.042    723
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.46 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 15.34 %
    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:  2.21 (0.34), residues: 618
  helix:  2.15 (0.28), residues: 340
  sheet:  2.53 (1.34), 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 I 281 
 PHE   0.013   0.002   PHE J  23 
 TYR   0.021   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
  114 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.636 
Fit side-chains
REVERT: I  268 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5917 (pm20)
REVERT: J   42 LYS cc_start: 0.5887 (OUTLIER) cc_final: 0.5141 (mmmt)
REVERT: J   92 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7460 (m-30)
  outliers start: 10
  outliers final: 7
  residues processed: 111
  average time/residue: 1.4414
  time to fit residues: 166.0672
Evaluate side-chains
  110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
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 I residue  268 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 31 optimal weight:    0.4980
   chunk 53 optimal weight:    2.9990
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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
I 155 ASN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 130 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.172077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.144850 restraints weight = 19489.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 2.19
r_work: 0.3674 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3591 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3590
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3590 r_free = 0.3590    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3590 r_free = 0.3590    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3590
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.0970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5261  Z= 0.236
  Angle     :  0.596   6.488   7121  Z= 0.306
  Chirality :  0.042   0.145    779
  Planarity :  0.005   0.034    905
  Dihedral  :  7.441  90.143    723
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.46 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 15.88 %
    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:  2.03 (0.34), residues: 618
  helix:  1.97 (0.28), residues: 340
  sheet:  2.48 (1.33), residues: 15
  loop :  0.57 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP I  11 
 HIS   0.006   0.001   HIS I 281 
 PHE   0.016   0.002   PHE J  81 
 TYR   0.023   0.002   TYR I  91 
 ARG   0.006   0.001   ARG H 268 

*********************** 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
  116 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.673 
Fit side-chains
REVERT: I  268 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.5900 (pm20)
REVERT: J   42 LYS cc_start: 0.5891 (OUTLIER) cc_final: 0.5169 (mmmt)
REVERT: J   92 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7475 (m-30)
  outliers start: 10
  outliers final: 6
  residues processed: 112
  average time/residue: 1.4332
  time to fit residues: 166.6708
Evaluate side-chains
  112 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
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  302 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.172993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.145619 restraints weight = 23807.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3806 rms_B_bonded: 2.33
r_work: 0.3679 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3596 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3594
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3594 r_free = 0.3594    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 = 0.3594 r_free = 0.3594    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3594
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
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   0.025   5261  Z= 0.175
  Angle     :  0.540   6.740   7121  Z= 0.276
  Chirality :  0.040   0.142    779
  Planarity :  0.004   0.034    905
  Dihedral  :  7.303  89.829    723
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.70 %
    Favored  : 82.13 %
  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:  2.62 (1.36), residues: 15
  loop :  0.60 (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
  113 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.580 
Fit side-chains
REVERT: I  124 GLN cc_start: 0.7112 (pt0) cc_final: 0.6090 (tp-100)
REVERT: I  268 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.5822 (pm20)
REVERT: J   42 LYS cc_start: 0.5870 (OUTLIER) cc_final: 0.5110 (mmmt)
REVERT: J   92 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7415 (m-30)
  outliers start: 12
  outliers final: 7
  residues processed: 109
  average time/residue: 1.3649
  time to fit residues: 154.5430
Evaluate side-chains
  110 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0970
   chunk 43 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0050
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.7996

-------------------------------------------------------------------------------
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**
J 130 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.173464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.145963 restraints weight = 21974.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3812 rms_B_bonded: 2.25
r_work: 0.3686 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3602 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3602
-------------------------------------------------------------------------------
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 = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3601
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
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   0.025   5261  Z= 0.173
  Angle     :  0.542   7.032   7121  Z= 0.276
  Chirality :  0.040   0.142    779
  Planarity :  0.005   0.034    905
  Dihedral  :  7.232  89.820    723
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.46 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 16.25 %
    Favored  : 82.13 %
  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:  2.24 (0.34), residues: 618
  helix:  2.16 (0.28), residues: 340
  sheet:  2.58 (1.34), residues: 15
  loop :  0.63 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP I  11 
 HIS   0.003   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 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
  109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.631 
Fit side-chains
REVERT: I  124 GLN cc_start: 0.7113 (pt0) cc_final: 0.6099 (tp-100)
REVERT: I  268 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5782 (pm20)
REVERT: J   42 LYS cc_start: 0.5866 (OUTLIER) cc_final: 0.5039 (mmmt)
REVERT: J   92 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7380 (m-30)
  outliers start: 9
  outliers final: 6
  residues processed: 106
  average time/residue: 1.3879
  time to fit residues: 152.9113
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  : 0.815 
-------------------------------------------------------------------------------
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  302 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0970
   chunk 51 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0270
   chunk 11 optimal weight:    7.9990
   overall best weight:    1.4240

-------------------------------------------------------------------------------
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 = 0.4129 r_free = 0.4129 target = 0.171886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.144706 restraints weight = 18649.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3797 rms_B_bonded: 2.12
r_work: 0.3674 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3589 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3588
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3588 r_free = 0.3588    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 = 0.3588 r_free = 0.3588    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3588
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.0989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5261  Z= 0.232
  Angle     :  0.599   7.070   7121  Z= 0.305
  Chirality :  0.042   0.145    779
  Planarity :  0.005   0.036    905
  Dihedral  :  7.359  89.303    723
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.29 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 15.88 %
    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:  2.03 (0.34), residues: 618
  helix:  1.98 (0.28), residues: 340
  sheet:  2.59 (1.33), residues: 15
  loop :  0.55 (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   0.019   0.002   PHE J  81 
 TYR   0.023   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: 7448.65 seconds
wall clock time: 131 minutes 24.09 seconds (7884.09 seconds total)