Starting phenix.real_space_refine
on Fri Aug 22 15:40:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p73_17516/08_2025/8p73_17516.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p73_17516/08_2025/8p73_17516.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p73_17516/08_2025/8p73_17516.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p73_17516/08_2025/8p73_17516.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p73_17516/08_2025/8p73_17516.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p73_17516/08_2025/8p73_17516.map"
  }
  resolution = 2.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    3292      2.51       5
     N     870      2.21       5
     O     976      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5169
  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: 2247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2247
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 275, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 260}
          Chain breaks: 2
    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: 60
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1, 30
          Unusual residues: {'X50': 1}
          Classifications: {'undetermined': 1}
      Conformer: "B"
        Number of residues, atoms: 1, 30
          Unusual residues: {'X58': 1}
          Classifications: {'undetermined': 1}
    Chain: "H"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "I"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 28
          Classifications: {'water': 28}
          Link IDs: {None: 27}
    Chain: "J"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 33
          Classifications: {'water': 33}
          Link IDs: {None: 32}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" C01AX50 J 401 " occ=0.29
      ... (28 atoms not shown)
      pdb=" O28AX50 J 401 " occ=0.29
    residue:
      pdb=" C01BX58 J 402 " occ=0.71
      ... (28 atoms not shown)
      pdb=" O28BX58 J 402 " occ=0.71
  Time building chain proxies: 1.49, per 1000 atoms: 0.29
  Number of scatterers: 5169
  At special positions: 0
  Unit cell: (84.075, 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     976      8.00
     N     870      7.00
     C    3292      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 198.3 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1188

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 3 sheets defined
      63.1% alpha, 4.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'H' and resid 262 through 275
      removed outlier: 4.151A  pdb=" N   GLY H 267 " --> pdb=" O   GLU H 264 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   GLY H 270 " --> pdb=" O   GLY H 267 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   TYR H 271 " --> pdb=" O   ARG H 268 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   LEU H 272 " --> pdb=" O   LEU H 269 " (cutoff:3.500A)
      removed outlier: 3.633A  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: 3.853A  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 37
    Processing helix  chain 'I' and resid 49 through 71
    Processing helix  chain 'I' and resid 76 through 93
      removed outlier: 3.890A  pdb=" N   ASN I  93 " --> pdb=" O   ARG I  89 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 100 through 117
      removed outlier: 3.511A  pdb=" N   LYS I 114 " --> pdb=" O   PHE I 110 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 121 through 127
    Processing helix  chain 'I' and resid 132 through 154
      removed outlier: 4.660A  pdb=" N   LEU I 148 " --> pdb=" O   LEU I 144 " (cutoff:3.500A)
      removed outlier: 4.676A  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: 3.604A  pdb=" N   THR I 201 " --> pdb=" O   ARG I 197 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 202 through 206
    Processing helix  chain 'I' and resid 208 through 224
    Processing helix  chain 'I' and resid 228 through 234
      removed outlier: 3.684A  pdb=" N   LEU I 232 " --> pdb=" O   MET I 228 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 243 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: 4.506A  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: 3.654A  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: 3.649A  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 14 through 20
      removed outlier: 6.098A  pdb=" N   VAL J  26 " --> pdb=" O   LEU J  18 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   ASP J  92 " --> pdb=" O   LEU J  77 " (cutoff:3.500A)
      removed outlier: 7.975A  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

    276 hydrogen bonds defined for protein.
    762 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.77

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1237
        1.33 -     1.45: 1023
        1.45 -     1.57: 2919
        1.57 -     1.69: 0
        1.69 -     1.81: 49
  Bond restraints: 5228
  Sorted by residual:
  bond pdb=" C08AX50 J 401 "
       pdb=" N09AX50 J 401 "
    ideal  model  delta    sigma   weight residual
    1.338  1.484 -0.146 2.00e-02 2.50e+03 5.33e+01
  bond pdb=" C18AX50 J 401 "
       pdb=" N19AX50 J 401 "
    ideal  model  delta    sigma   weight residual
    1.351  1.495 -0.144 2.00e-02 2.50e+03 5.20e+01
  bond pdb=" C08BX58 J 402 "
       pdb=" N09BX58 J 402 "
    ideal  model  delta    sigma   weight residual
    1.342  1.458 -0.116 2.00e-02 2.50e+03 3.36e+01
  bond pdb=" C18BX58 J 402 "
       pdb=" N19BX58 J 402 "
    ideal  model  delta    sigma   weight residual
    1.358  1.460 -0.102 2.00e-02 2.50e+03 2.60e+01
  bond pdb=" C30BX58 J 402 "
       pdb=" N07BX58 J 402 "
    ideal  model  delta    sigma   weight residual
    1.383  1.302  0.081 2.00e-02 2.50e+03 1.66e+01
  ... (remaining 5223 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 6870
        1.71 -     3.41: 163
        3.41 -     5.12: 31
        5.12 -     6.82: 9
        6.82 -     8.53: 6
  Bond angle restraints: 7079
  Sorted by residual:
  angle pdb=" CA  LYS I  29 "
        pdb=" CB  LYS I  29 "
        pdb=" CG  LYS I  29 "
      ideal   model   delta    sigma   weight residual
     114.10  122.63   -8.53 2.00e+00 2.50e-01 1.82e+01
  angle pdb=" CG  ARG I 279 "
        pdb=" CD  ARG I 279 "
        pdb=" NE  ARG I 279 "
      ideal   model   delta    sigma   weight residual
     112.00  119.81   -7.81 2.20e+00 2.07e-01 1.26e+01
  angle pdb=" CA  TYR I  91 "
        pdb=" CB  TYR I  91 "
        pdb=" CG  TYR I  91 "
      ideal   model   delta    sigma   weight residual
     113.90  108.41    5.49 1.80e+00 3.09e-01 9.30e+00
  angle pdb=" CB  MET J  94 "
        pdb=" CG  MET J  94 "
        pdb=" SD  MET J  94 "
      ideal   model   delta    sigma   weight residual
     112.70  120.99   -8.29 3.00e+00 1.11e-01 7.64e+00
  angle pdb=" C18BX58 J 402 "
        pdb=" N19BX58 J 402 "
        pdb=" C20BX58 J 402 "
      ideal   model   delta    sigma   weight residual
     125.44  117.87    7.57 3.00e+00 1.11e-01 6.37e+00
  ... (remaining 7074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 2765
       17.67 -    35.33: 303
       35.33 -    52.99: 76
       52.99 -    70.66: 18
       70.66 -    88.32: 11
  Dihedral angle restraints: 3173
    sinusoidal: 1339
      harmonic: 1834
  Sorted by residual:
  dihedral pdb=" CA  THR J 175 "
           pdb=" C   THR J 175 "
           pdb=" N   ARG J 176 "
           pdb=" CA  ARG J 176 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.37  -18.63     0      5.00e+00 4.00e-02 1.39e+01
  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  162.87   17.13     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  THR I 176 "
           pdb=" C   THR I 176 "
           pdb=" N   ARG I 177 "
           pdb=" CA  ARG I 177 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.05  -16.95     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 3170 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 490
       0.032 -    0.064: 184
       0.064 -    0.096: 70
       0.096 -    0.128: 24
       0.128 -    0.160: 6
  Chirality restraints: 774
  Sorted by residual:
  chirality pdb=" C21BX58 J 402 "
            pdb=" C23BX58 J 402 "
            pdb=" C27BX58 J 402 "
            pdb=" O22BX58 J 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.63    2.47    0.16 2.00e-01 2.50e+01 6.42e-01
  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 5.09e-01
  chirality pdb=" CA  PRO I 101 "
            pdb=" N   PRO I 101 "
            pdb=" C   PRO I 101 "
            pdb=" CB  PRO I 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.92e-01
  ... (remaining 771 not shown)

  Planarity restraints: 898
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG I 279 "    0.258 9.50e-02 1.11e+02   1.16e-01 8.25e+00
        pdb=" NE  ARG I 279 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG I 279 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG I 279 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG I 279 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP I 116 "   -0.010 2.00e-02 2.50e+03   1.94e-02 3.78e+00
        pdb=" CG  ASP I 116 "    0.034 2.00e-02 2.50e+03
        pdb=" OD1 ASP I 116 "   -0.012 2.00e-02 2.50e+03
        pdb=" OD2 ASP I 116 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG I 165 "    0.024 5.00e-02 4.00e+02   3.68e-02 2.17e+00
        pdb=" N   PRO I 166 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO I 166 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO I 166 "    0.021 5.00e-02 4.00e+02
  ... (remaining 895 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 262
        2.73 -     3.27: 5428
        3.27 -     3.81: 9509
        3.81 -     4.36: 11586
        4.36 -     4.90: 18900
  Nonbonded interactions: 45685
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU J  62 "
            pdb=" O   HOH J 501 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OD1 ASP J 104 "
            pdb=" OG  SER J 106 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   HOH J 532 "
            pdb=" O   HOH J 533 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OG1 THR J 231 "
            pdb=" O   LYS J 250 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OD2 ASP J  97 "
            pdb=" O   HOH J 502 "
     model   vdw
     2.256 3.040
  ... (remaining 45680 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=0.29 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:             3.710
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.930
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
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   0.146   5228  Z= 0.302
  Angle     :  0.689   8.526   7079  Z= 0.325
  Chirality :  0.042   0.160    774
  Planarity :  0.006   0.116    898
  Dihedral  : 16.691  88.324   1985
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.47 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 17.82 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.34), residues: 612
  helix:  1.67 (0.28), residues: 334
  sheet:  0.37 (1.51), residues: 15
  loop :  0.15 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 268 
 TYR   0.023   0.002   TYR I  91 
 PHE   0.015   0.002   PHE I  30 
 TRP   0.010   0.002   TRP J 132 
 HIS   0.005   0.001   HIS J 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00626 ( 5228)
  covalent geometry    : angle       0.68906 ( 7079)
  hydrogen bonds       : bond        0.13269 (  276)
  hydrogen bonds       : angle       6.12240 (  762)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 8
  residues processed: 93
  average time/residue: 0.7124
  time to fit residues: 68.5425
Evaluate side-chains
  92 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  171 LEU
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain I residue  230 SER
Chi-restraints excluded: chain I residue  242 ARG
Chi-restraints excluded: chain I residue  254 SER
Chi-restraints excluded: chain I residue  274 LYS
Chi-restraints excluded: chain J residue  242 SER
Chi-restraints excluded: chain J residue  248 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0070
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.9802

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.179475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.156349 restraints weight = 21262.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 2.43
r_work: 0.3677 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3673
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3673 r_free = 0.3673    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3673 r_free = 0.3673    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3673
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.0633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5228  Z= 0.136
  Angle     :  0.559   7.598   7079  Z= 0.287
  Chirality :  0.041   0.140    774
  Planarity :  0.005   0.037    898
  Dihedral  :  5.968  59.651    750
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.31 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 17.27 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.77 (0.35), residues: 612
  helix:  1.87 (0.29), residues: 344
  sheet:  0.05 (1.53), residues: 15
  loop :  0.39 (0.40), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I  31 
 TYR   0.022   0.002   TYR I  91 
 PHE   0.016   0.002   PHE J  91 
 TRP   0.008   0.001   TRP I  11 
 HIS   0.005   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 5228)
  covalent geometry    : angle       0.55932 ( 7079)
  hydrogen bonds       : bond        0.05039 (  276)
  hydrogen bonds       : angle       4.85401 (  762)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 1
  residues processed: 92
  average time/residue: 0.7189
  time to fit residues: 68.5035
Evaluate side-chains
  86 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  218 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   chunk 35 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0370
   chunk 10 optimal weight:    5.9990
   overall best weight:    1.9462

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS
J 297 ASN

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 = 0.177465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.155043 restraints weight = 16144.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3881 rms_B_bonded: 1.97
r_work: 0.3686 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3591 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3586
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3586 r_free = 0.3586    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3586
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.0643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   5228  Z= 0.192
  Angle     :  0.636   8.932   7079  Z= 0.325
  Chirality :  0.043   0.147    774
  Planarity :  0.005   0.036    898
  Dihedral  :  5.670  59.303    736
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.80 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 17.45 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.34), residues: 612
  helix:  1.54 (0.28), residues: 343
  sheet:  0.10 (1.58), residues: 15
  loop :  0.15 (0.40), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG I  23 
 TYR   0.027   0.002   TYR I  91 
 PHE   0.017   0.003   PHE J  91 
 TRP   0.010   0.002   TRP I  11 
 HIS   0.006   0.002   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 5228)
  covalent geometry    : angle       0.63644 ( 7079)
  hydrogen bonds       : bond        0.05507 (  276)
  hydrogen bonds       : angle       4.96441 (  762)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.230 
Fit side-chains
REVERT: H  276 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.5598 (ttt-90)
REVERT: I  250 ASP cc_start: 0.6388 (m-30) cc_final: 0.6076 (m-30)
REVERT: J  169 TYR cc_start: 0.6481 (m-80) cc_final: 0.5920 (m-80)
  outliers start: 9
  outliers final: 3
  residues processed: 92
  average time/residue: 0.7296
  time to fit residues: 69.3662
Evaluate side-chains
  89 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  276 ARG
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain J residue  248 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9980
   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 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.179376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.156783 restraints weight = 17555.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3904 rms_B_bonded: 2.19
r_work: 0.3705 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3702
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3702 r_free = 0.3702    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3702 r_free = 0.3702    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3702
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.0751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5228  Z= 0.130
  Angle     :  0.558   7.659   7079  Z= 0.285
  Chirality :  0.040   0.143    774
  Planarity :  0.005   0.038    898
  Dihedral  :  5.494  59.867    736
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.14 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.27 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.35), residues: 612
  helix:  1.82 (0.29), residues: 344
  sheet:  0.20 (1.55), residues: 15
  loop :  0.29 (0.40), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I  23 
 TYR   0.022   0.002   TYR I  91 
 PHE   0.015   0.002   PHE J  91 
 TRP   0.009   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 5228)
  covalent geometry    : angle       0.55777 ( 7079)
  hydrogen bonds       : bond        0.04695 (  276)
  hydrogen bonds       : angle       4.69378 (  762)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.207 
Fit side-chains
REVERT: H  251 LEU cc_start: 0.5535 (OUTLIER) cc_final: 0.5311 (tp)
REVERT: H  276 ARG cc_start: 0.6155 (OUTLIER) cc_final: 0.5535 (ttt-90)
REVERT: I  138 LYS cc_start: 0.7147 (ttmm) cc_final: 0.6891 (mttm)
REVERT: J  169 TYR cc_start: 0.6336 (m-80) cc_final: 0.5847 (m-80)
  outliers start: 10
  outliers final: 2
  residues processed: 93
  average time/residue: 0.6734
  time to fit residues: 64.8034
Evaluate side-chains
  92 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  251 LEU
Chi-restraints excluded: chain H residue  276 ARG
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  218 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 51 optimal weight:    0.4980
   chunk 48 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   chunk 0 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS
J 297 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.179877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.156124 restraints weight = 22101.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3894 rms_B_bonded: 2.48
r_work: 0.3703 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3699
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3699 r_free = 0.3699    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3699 r_free = 0.3699    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3699
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.0877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5228  Z= 0.121
  Angle     :  0.537   7.523   7079  Z= 0.275
  Chirality :  0.040   0.140    774
  Planarity :  0.004   0.039    898
  Dihedral  :  5.402  59.388    736
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  0.98 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.64 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.35), residues: 612
  helix:  1.92 (0.29), residues: 345
  sheet:  0.41 (1.51), residues: 15
  loop :  0.32 (0.40), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 268 
 TYR   0.020   0.001   TYR I  91 
 PHE   0.014   0.002   PHE J  91 
 TRP   0.008   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 5228)
  covalent geometry    : angle       0.53707 ( 7079)
  hydrogen bonds       : bond        0.04448 (  276)
  hydrogen bonds       : angle       4.57872 (  762)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.173 
Fit side-chains
REVERT: H  276 ARG cc_start: 0.6136 (OUTLIER) cc_final: 0.5490 (ttt-90)
REVERT: I  138 LYS cc_start: 0.7209 (ttmm) cc_final: 0.6909 (mttm)
REVERT: J   11 ARG cc_start: 0.5768 (ptt-90) cc_final: 0.5161 (ttt90)
REVERT: J   83 HIS cc_start: 0.5947 (OUTLIER) cc_final: 0.5609 (m-70)
REVERT: J  169 TYR cc_start: 0.6282 (m-80) cc_final: 0.5823 (m-80)
  outliers start: 11
  outliers final: 2
  residues processed: 92
  average time/residue: 0.6660
  time to fit residues: 63.2941
Evaluate side-chains
  88 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  276 ARG
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain J residue   83 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 24 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 17 optimal weight:    0.2980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS
J 297 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.179830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.156938 restraints weight = 18198.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3905 rms_B_bonded: 2.35
r_work: 0.3714 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3713
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3713 r_free = 0.3713    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3713 r_free = 0.3713    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3713
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.0957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5228  Z= 0.121
  Angle     :  0.542   7.408   7079  Z= 0.277
  Chirality :  0.040   0.139    774
  Planarity :  0.004   0.040    898
  Dihedral  :  5.367  59.638    736
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  0.98 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 17.82 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.35), residues: 612
  helix:  1.95 (0.29), residues: 345
  sheet:  0.60 (1.55), residues: 15
  loop :  0.35 (0.40), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 268 
 TYR   0.021   0.001   TYR I  91 
 PHE   0.014   0.002   PHE J 185 
 TRP   0.008   0.001   TRP I  11 
 HIS   0.004   0.001   HIS J 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 5228)
  covalent geometry    : angle       0.54203 ( 7079)
  hydrogen bonds       : bond        0.04391 (  276)
  hydrogen bonds       : angle       4.53380 (  762)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.133 
Fit side-chains
REVERT: H  276 ARG cc_start: 0.6124 (OUTLIER) cc_final: 0.5473 (ttt-90)
REVERT: J   11 ARG cc_start: 0.5844 (ptt-90) cc_final: 0.5211 (ttt90)
REVERT: J   83 HIS cc_start: 0.5939 (OUTLIER) cc_final: 0.5596 (m-70)
REVERT: J  169 TYR cc_start: 0.6267 (m-80) cc_final: 0.5801 (m-80)
  outliers start: 8
  outliers final: 3
  residues processed: 89
  average time/residue: 0.7230
  time to fit residues: 66.4383
Evaluate side-chains
  87 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  276 ARG
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain I residue  227 THR
Chi-restraints excluded: chain I residue  237 MET
Chi-restraints excluded: chain J residue   83 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS
J 297 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.177647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.154994 restraints weight = 12375.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 1.59
r_work: 0.3727 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3632 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3628
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3628 r_free = 0.3628    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3628 r_free = 0.3628    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3628
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.0814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5228  Z= 0.177
  Angle     :  0.628   8.569   7079  Z= 0.319
  Chirality :  0.042   0.144    774
  Planarity :  0.005   0.037    898
  Dihedral  :  5.589  59.395    736
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.63 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 19.09 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.34), residues: 612
  helix:  1.64 (0.28), residues: 344
  sheet:  0.72 (1.60), residues: 15
  loop :  0.20 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 268 
 TYR   0.027   0.002   TYR I  91 
 PHE   0.017   0.003   PHE J  17 
 TRP   0.010   0.002   TRP I  11 
 HIS   0.007   0.002   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 5228)
  covalent geometry    : angle       0.62845 ( 7079)
  hydrogen bonds       : bond        0.05166 (  276)
  hydrogen bonds       : angle       4.78085 (  762)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.185 
Fit side-chains
REVERT: H  276 ARG cc_start: 0.6179 (OUTLIER) cc_final: 0.5572 (ttt-90)
REVERT: J   11 ARG cc_start: 0.5713 (ptt-90) cc_final: 0.5137 (ttt90)
REVERT: J   83 HIS cc_start: 0.6033 (OUTLIER) cc_final: 0.5693 (m-70)
REVERT: J  169 TYR cc_start: 0.6394 (m-80) cc_final: 0.5908 (m-80)
  outliers start: 5
  outliers final: 3
  residues processed: 86
  average time/residue: 0.6417
  time to fit residues: 56.9120
Evaluate side-chains
  86 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  276 ARG
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain I residue  227 THR
Chi-restraints excluded: chain J residue   83 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 38 optimal weight:    9.9990
   chunk 4 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.177893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.154347 restraints weight = 16551.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 2.08
r_work: 0.3704 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3608 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3601
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3601 r_free = 0.3601    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3601 r_free = 0.3601    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3601
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.0813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5228  Z= 0.168
  Angle     :  0.626   8.562   7079  Z= 0.316
  Chirality :  0.042   0.143    774
  Planarity :  0.005   0.037    898
  Dihedral  :  5.633  59.317    736
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.31 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 18.73 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.34), residues: 612
  helix:  1.60 (0.28), residues: 344
  sheet:  0.92 (1.70), residues: 15
  loop :  0.14 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 268 
 TYR   0.025   0.002   TYR I  91 
 PHE   0.021   0.002   PHE J  17 
 TRP   0.010   0.002   TRP I  11 
 HIS   0.006   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 5228)
  covalent geometry    : angle       0.62580 ( 7079)
  hydrogen bonds       : bond        0.05078 (  276)
  hydrogen bonds       : angle       4.76395 (  762)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.210 
Fit side-chains
REVERT: H  276 ARG cc_start: 0.6167 (OUTLIER) cc_final: 0.5581 (ttt-90)
REVERT: J   11 ARG cc_start: 0.5726 (ptt-90) cc_final: 0.5099 (ttt180)
REVERT: J   83 HIS cc_start: 0.6147 (OUTLIER) cc_final: 0.5809 (m-70)
REVERT: J  169 TYR cc_start: 0.6446 (m-80) cc_final: 0.5913 (m-80)
  outliers start: 6
  outliers final: 3
  residues processed: 87
  average time/residue: 0.7409
  time to fit residues: 66.6437
Evaluate side-chains
  88 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  276 ARG
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain I residue  227 THR
Chi-restraints excluded: chain J residue   83 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.176846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.154049 restraints weight = 18581.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.3872 rms_B_bonded: 2.22
r_work: 0.3672 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3666
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3666 r_free = 0.3666    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3666 r_free = 0.3666    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3666
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.0809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   5228  Z= 0.209
  Angle     :  0.690   9.307   7079  Z= 0.348
  Chirality :  0.044   0.146    774
  Planarity :  0.006   0.037    898
  Dihedral  :  5.773  59.103    736
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.47 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 19.09 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.34), residues: 612
  helix:  1.39 (0.28), residues: 343
  sheet:  1.01 (1.75), residues: 15
  loop : -0.04 (0.39), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H 268 
 TYR   0.029   0.002   TYR I  91 
 PHE   0.023   0.003   PHE J  17 
 TRP   0.010   0.002   TRP J 237 
 HIS   0.007   0.002   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 5228)
  covalent geometry    : angle       0.68984 ( 7079)
  hydrogen bonds       : bond        0.05541 (  276)
  hydrogen bonds       : angle       4.91947 (  762)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.180 
Fit side-chains
REVERT: H  276 ARG cc_start: 0.6176 (OUTLIER) cc_final: 0.5554 (ttt-90)
REVERT: I  250 ASP cc_start: 0.6290 (m-30) cc_final: 0.5993 (m-30)
REVERT: J   11 ARG cc_start: 0.5746 (ptt-90) cc_final: 0.5193 (ttt180)
REVERT: J   83 HIS cc_start: 0.5955 (OUTLIER) cc_final: 0.5620 (m-70)
REVERT: J  169 TYR cc_start: 0.6393 (m-80) cc_final: 0.6053 (m-80)
  outliers start: 5
  outliers final: 3
  residues processed: 89
  average time/residue: 0.7672
  time to fit residues: 70.4622
Evaluate side-chains
  90 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  276 ARG
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain I residue  227 THR
Chi-restraints excluded: chain J residue   83 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 3 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.176798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.153353 restraints weight = 16849.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 2.15
r_work: 0.3687 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3591 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3587
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3587 r_free = 0.3587    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3587 r_free = 0.3587    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3587
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.0861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   5228  Z= 0.217
  Angle     :  0.700   9.127   7079  Z= 0.354
  Chirality :  0.044   0.146    774
  Planarity :  0.006   0.039    898
  Dihedral  :  5.847  58.909    736
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.63 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 18.73 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.34), residues: 612
  helix:  1.29 (0.28), residues: 343
  sheet:  1.01 (1.72), residues: 15
  loop : -0.14 (0.39), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H 268 
 TYR   0.029   0.002   TYR I  91 
 PHE   0.025   0.003   PHE J  17 
 TRP   0.010   0.002   TRP I  11 
 HIS   0.007   0.002   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 5228)
  covalent geometry    : angle       0.70002 ( 7079)
  hydrogen bonds       : bond        0.05614 (  276)
  hydrogen bonds       : angle       4.95541 (  762)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.205 
Fit side-chains
REVERT: H  276 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.5575 (ttt-90)
REVERT: I  250 ASP cc_start: 0.6394 (m-30) cc_final: 0.6102 (m-30)
REVERT: J   11 ARG cc_start: 0.5725 (OUTLIER) cc_final: 0.5125 (ttt180)
REVERT: J   83 HIS cc_start: 0.6155 (OUTLIER) cc_final: 0.5804 (m-70)
REVERT: J  169 TYR cc_start: 0.6490 (m-80) cc_final: 0.6037 (m-80)
  outliers start: 7
  outliers final: 4
  residues processed: 90
  average time/residue: 0.7486
  time to fit residues: 69.6581
Evaluate side-chains
  93 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  276 ARG
Chi-restraints excluded: chain I residue  105 MET
Chi-restraints excluded: chain I residue  218 LEU
Chi-restraints excluded: chain I residue  227 THR
Chi-restraints excluded: chain J residue   11 ARG
Chi-restraints excluded: chain J residue   83 HIS
Chi-restraints excluded: chain J residue  248 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 48 optimal weight:    0.5980
   chunk 7 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
H 307 GLN
I 136 GLN
** J 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 258 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.178627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.154880 restraints weight = 19975.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3880 rms_B_bonded: 2.40
r_work: 0.3698 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3694
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3694 r_free = 0.3694    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3694 r_free = 0.3694    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3694
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.0838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5228  Z= 0.147
  Angle     :  0.614   7.975   7079  Z= 0.311
  Chirality :  0.041   0.147    774
  Planarity :  0.005   0.037    898
  Dihedral  :  5.655  59.669    736
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.31 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 18.73 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.35), residues: 612
  helix:  1.64 (0.29), residues: 344
  sheet:  0.91 (1.67), residues: 15
  loop :  0.06 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 268 
 TYR   0.023   0.002   TYR I  91 
 PHE   0.023   0.002   PHE J  17 
 TRP   0.011   0.002   TRP I  11 
 HIS   0.005   0.001   HIS J 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5228)
  covalent geometry    : angle       0.61350 ( 7079)
  hydrogen bonds       : bond        0.04828 (  276)
  hydrogen bonds       : angle       4.69943 (  762)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2737.70 seconds
wall clock time: 47 minutes 26.45 seconds (2846.45 seconds total)