Starting phenix.real_space_refine
on Wed Jul 23 22:38:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v0t_26950/07_2025/7v0t_26950.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v0t_26950/07_2025/7v0t_26950.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v0t_26950/07_2025/7v0t_26950.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v0t_26950/07_2025/7v0t_26950.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v0t_26950/07_2025/7v0t_26950.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v0t_26950/07_2025/7v0t_26950.cif"
  }
  resolution = 2.7
  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=   0.001 sd=   0.277
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      12      5.16       5
     C    2941      2.51       5
     N     805      2.21       5
     O     900      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 4658
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "E"
      Number of atoms: 2276
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2276
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 19, 'TRANS': 267}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 2343
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2343
          Classifications: {'peptide': 297}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 16, 'TRANS': 280}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "E"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
    Chain: "C"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 34
          Classifications: {'water': 34}
          Link IDs: {None: 33}
  Time building chain proxies: 3.92, per 1000 atoms: 0.84
  Number of scatterers: 4658
  At special positions: 0
  Unit cell: (89.225, 82.585, 75.53, 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      12     16.00
     O     900      8.00
     N     805      7.00
     C    2941      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: 1.50
  Conformation dependent library (CDL) restraints added in 595.8 milliseconds
  

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1108

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 3 sheets defined
      41.3% alpha, 12.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'E' and resid 104 through 116
      removed outlier: 3.817A  pdb=" N   LYS E 116 " --> pdb=" O   ARG E 112 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 127 through 142
    Processing helix  chain 'E' and resid 146 through 148
      No H-bonds generated for 'chain 'E' and resid 146 through 148'
    Processing helix  chain 'E' and resid 149 through 158
    Processing helix  chain 'E' and resid 163 through 167
    Processing helix  chain 'E' and resid 194 through 201
    Processing helix  chain 'E' and resid 277 through 291
    Processing helix  chain 'E' and resid 291 through 300
    Processing helix  chain 'E' and resid 303 through 317
      removed outlier: 3.738A  pdb=" N   LEU E 307 " --> pdb=" O   SER E 303 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 328 through 334
    Processing helix  chain 'E' and resid 335 through 349
      removed outlier: 4.147A  pdb=" N   SER E 349 " --> pdb=" O   ARG E 345 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 47
    Processing helix  chain 'C' and resid 103 through 116
      removed outlier: 3.842A  pdb=" N   LYS C 116 " --> pdb=" O   ARG C 112 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 127 through 142
    Processing helix  chain 'C' and resid 146 through 148
      No H-bonds generated for 'chain 'C' and resid 146 through 148'
    Processing helix  chain 'C' and resid 149 through 158
    Processing helix  chain 'C' and resid 163 through 170
      removed outlier: 3.588A  pdb=" N   LEU C 167 " --> pdb=" O   HIS C 163 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   GLU C 168 " --> pdb=" O   ALA C 164 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   ALA C 169 " --> pdb=" O   GLY C 165 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 194 through 201
    Processing helix  chain 'C' and resid 277 through 291
    Processing helix  chain 'C' and resid 291 through 301
    Processing helix  chain 'C' and resid 303 through 317
      removed outlier: 3.696A  pdb=" N   LEU C 307 " --> pdb=" O   SER C 303 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 327 through 334
    Processing helix  chain 'C' and resid 334 through 343
      removed outlier: 4.139A  pdb=" N   VAL C 338 " --> pdb=" O   SER C 334 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 59 through 67
      removed outlier: 6.493A  pdb=" N   VAL E  59 " --> pdb=" O   ARG E  80 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   ARG E  80 " --> pdb=" O   VAL E  59 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   LEU E  61 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 85 through 87
    current: chain 'E' and resid 184 through 185
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 184 through 185
    current: chain 'E' and resid 262 through 270
    Processing sheet with id=AA2, first strand: chain 'E' and resid 102 through 103
    Processing sheet with id=AA3, first strand: chain 'C' and resid 56 through 66
      removed outlier: 6.556A  pdb=" N   VAL C  59 " --> pdb=" O   ARG C  80 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   ARG C  80 " --> pdb=" O   VAL C  59 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   LEU C  61 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 85 through 87
    current: chain 'C' and resid 224 through 234
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 224 through 234
    current: chain 'C' and resid 262 through 270

    164 hydrogen bonds defined for protein.
    468 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: 1.15

  Time building geometry restraints manager: 1.77 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1574
        1.34 -     1.46: 884
        1.46 -     1.58: 2235
        1.58 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 4713
  Sorted by residual:
  bond pdb=" N   PRO C 221 "
       pdb=" CA  PRO C 221 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.31e-02 5.83e+03 1.61e+00
  bond pdb=" CB  GLN E 124 "
       pdb=" CG  GLN E 124 "
    ideal  model  delta    sigma   weight residual
    1.520  1.556 -0.036 3.00e-02 1.11e+03 1.44e+00
  bond pdb=" CG1 ILE C 140 "
       pdb=" CD1 ILE C 140 "
    ideal  model  delta    sigma   weight residual
    1.513  1.471  0.042 3.90e-02 6.57e+02 1.15e+00
  bond pdb=" CA  ILE C 216 "
       pdb=" CB  ILE C 216 "
    ideal  model  delta    sigma   weight residual
    1.540  1.568 -0.028 2.70e-02 1.37e+03 1.08e+00
  bond pdb=" CG  GLN E 124 "
       pdb=" CD  GLN E 124 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.07e+00
  ... (remaining 4708 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 6198
        1.43 -     2.87: 160
        2.87 -     4.30: 33
        4.30 -     5.74: 9
        5.74 -     7.17: 5
  Bond angle restraints: 6405
  Sorted by residual:
  angle pdb=" N   ASN C  91 "
        pdb=" CA  ASN C  91 "
        pdb=" C   ASN C  91 "
      ideal   model   delta    sigma   weight residual
     114.09  109.26    4.83 1.55e+00 4.16e-01 9.69e+00
  angle pdb=" CB  GLN E 124 "
        pdb=" CG  GLN E 124 "
        pdb=" CD  GLN E 124 "
      ideal   model   delta    sigma   weight residual
     112.60  117.66   -5.06 1.70e+00 3.46e-01 8.86e+00
  angle pdb=" C   LEU C 335 "
        pdb=" N   VAL C 336 "
        pdb=" CA  VAL C 336 "
      ideal   model   delta    sigma   weight residual
     120.33  122.60   -2.27 8.00e-01 1.56e+00 8.06e+00
  angle pdb=" CA  GLN E 124 "
        pdb=" CB  GLN E 124 "
        pdb=" CG  GLN E 124 "
      ideal   model   delta    sigma   weight residual
     114.10  119.52   -5.42 2.00e+00 2.50e-01 7.34e+00
  angle pdb=" CA  PRO C 271 "
        pdb=" C   PRO C 271 "
        pdb=" N   GLU C 272 "
      ideal   model   delta    sigma   weight residual
     114.74  117.11   -2.37 1.03e+00 9.43e-01 5.30e+00
  ... (remaining 6400 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 2432
       17.95 -    35.90: 294
       35.90 -    53.86: 99
       53.86 -    71.81: 29
       71.81 -    89.76: 17
  Dihedral angle restraints: 2871
    sinusoidal: 1175
      harmonic: 1696
  Sorted by residual:
  dihedral pdb=" CA  TRP E  81 "
           pdb=" C   TRP E  81 "
           pdb=" N   VAL E  82 "
           pdb=" CA  VAL E  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.25   22.75     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CG  ARG C 246 "
           pdb=" CD  ARG C 246 "
           pdb=" NE  ARG C 246 "
           pdb=" CZ  ARG C 246 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -134.83   44.83     2      1.50e+01 4.44e-03 1.06e+01
  dihedral pdb=" CB  GLU C  32 "
           pdb=" CG  GLU C  32 "
           pdb=" CD  GLU C  32 "
           pdb=" OE1 GLU C  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.72  -88.72     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 2868 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 567
       0.045 -    0.090: 123
       0.090 -    0.135: 38
       0.135 -    0.180: 4
       0.180 -    0.225: 1
  Chirality restraints: 733
  Sorted by residual:
  chirality pdb=" CB  ILE C 216 "
            pdb=" CA  ILE C 216 "
            pdb=" CG1 ILE C 216 "
            pdb=" CG2 ILE C 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CB  ILE E 276 "
            pdb=" CA  ILE E 276 "
            pdb=" CG1 ILE E 276 "
            pdb=" CG2 ILE E 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.16 2.00e-01 2.50e+01 6.32e-01
  chirality pdb=" CA  VAL E  82 "
            pdb=" N   VAL E  82 "
            pdb=" C   VAL E  82 "
            pdb=" CB  VAL E  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.88e-01
  ... (remaining 730 not shown)

  Planarity restraints: 840
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA E 273 "    0.024 5.00e-02 4.00e+02   3.64e-02 2.12e+00
        pdb=" N   PRO E 274 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO E 274 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO E 274 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 326 "    0.022 5.00e-02 4.00e+02   3.31e-02 1.76e+00
        pdb=" N   PRO C 327 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO C 327 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 327 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 146 "   -0.022 5.00e-02 4.00e+02   3.30e-02 1.74e+00
        pdb=" N   PRO C 147 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO C 147 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 147 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 837 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 138
        2.70 -     3.25: 4322
        3.25 -     3.80: 7907
        3.80 -     4.35: 10331
        4.35 -     4.90: 16454
  Nonbonded interactions: 39152
  Sorted by model distance:
  nonbonded pdb=" OG1 THR E 179 "
            pdb=" O   ASP E 183 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" NE2 HIS E 275 "
            pdb=" OE1 GLU C 312 "
     model   vdw
     2.195 3.120
  nonbonded pdb=" NH1 ARG C 233 "
            pdb=" O   HOH C1001 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" O   TYR C  46 "
            pdb=" O   HOH C1002 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OE1 GLU C 225 "
            pdb=" OH  TYR C 299 "
     model   vdw
     2.293 3.040
  ... (remaining 39147 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
Found NCS groups:
ncs_group {
  reference = (chain 'C' and (resid 56 through 203 or resid 217 through 348))
  selection = (chain 'E' and ((resid 56 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 57 through 181 or resid 192 through 348))
}

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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.200
  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:          0.350
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.990
  Find NCS groups from input model:        0.180
  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:             0.010
  Load rotamer database and sin/cos tables:12.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
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      :  0.004   0.042   4713  Z= 0.165
  Angle     :  0.631   7.174   6405  Z= 0.333
  Chirality :  0.042   0.225    733
  Planarity :  0.005   0.036    840
  Dihedral  : 19.430  89.760   1763
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  1.57 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 27.79 %
    Favored  : 68.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.57 (0.33), residues: 574
  helix:  0.62 (0.34), residues: 219
  sheet:  1.76 (0.57), residues: 84
  loop : -0.18 (0.35), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E  81 
 HIS   0.003   0.001   HIS E 163 
 PHE   0.022   0.002   PHE C 314 
 TYR   0.019   0.002   TYR E 278 
 ARG   0.004   0.001   ARG E 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15437 (  164)
  hydrogen bonds       : angle       5.85728 (  468)
  covalent geometry    : bond        0.00374 ( 4713)
  covalent geometry    : angle       0.63087 ( 6405)

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.488 
Fit side-chains
REVERT: C   83 GLN cc_start: 0.7179 (mt0) cc_final: 0.6971 (mp10)
REVERT: C  109 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8112 (mp0)
  outliers start: 17
  outliers final: 12
  residues processed: 84
  average time/residue: 1.4563
  time to fit residues: 126.7567
Evaluate side-chains
  82 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain E residue  223 ASP
Chi-restraints excluded: chain C residue   50 SER
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  127 SER
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  194 SER
Chi-restraints excluded: chain C residue  224 SER
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  265 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 48 optimal weight:    0.0010
   chunk 43 optimal weight:    1.9990
   chunk 23 optimal weight:   20.0000
   chunk 14 optimal weight:    9.9990
   chunk 29 optimal weight:    7.9990
   chunk 44 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 28 optimal weight:   10.0000
   overall best weight:    1.3792

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

Flipped N/Q/H residues before XYZ refinement:
E  83 GLN
E 275 HIS
C 124 GLN
** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 198 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.178276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.137121 restraints weight = 4610.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 2.20
r_work: 0.3125 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.0699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4713  Z= 0.115
  Angle     :  0.517   6.553   6405  Z= 0.257
  Chirality :  0.039   0.153    733
  Planarity :  0.004   0.030    840
  Dihedral  :  6.947  55.006    648
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 25.96 %
    Favored  : 69.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.00 (0.34), residues: 574
  helix:  1.12 (0.35), residues: 220
  sheet:  1.89 (0.58), residues: 84
  loop : -0.04 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  81 
 HIS   0.002   0.001   HIS E 309 
 PHE   0.018   0.002   PHE C 314 
 TYR   0.012   0.001   TYR E 278 
 ARG   0.003   0.000   ARG E  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03985 (  164)
  hydrogen bonds       : angle       4.53119 (  468)
  covalent geometry    : bond        0.00256 ( 4713)
  covalent geometry    : angle       0.51682 ( 6405)

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.503 
Fit side-chains
REVERT: E   63 GLU cc_start: 0.7839 (tp30) cc_final: 0.7572 (mm-30)
REVERT: C  114 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8075 (m-80)
  outliers start: 20
  outliers final: 11
  residues processed: 84
  average time/residue: 1.4413
  time to fit residues: 125.1059
Evaluate side-chains
  81 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue  114 PHE
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain E residue  223 ASP
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  114 PHE
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  256 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 14 optimal weight:   10.0000
   chunk 3 optimal weight:    8.9990
   chunk 43 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 15 optimal weight:   20.0000
   chunk 51 optimal weight:    8.9990
   chunk 33 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
E 275 HIS
C 148 GLN
C 198 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.181516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.140934 restraints weight = 4676.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 1.79
r_work: 0.3128 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.0887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   4713  Z= 0.208
  Angle     :  0.591   8.233   6405  Z= 0.294
  Chirality :  0.042   0.150    733
  Planarity :  0.004   0.033    840
  Dihedral  :  6.737  59.847    639
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 25.56 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.84 (0.34), residues: 574
  helix:  1.03 (0.35), residues: 220
  sheet:  1.90 (0.57), residues: 84
  loop : -0.21 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E  81 
 HIS   0.003   0.001   HIS E 309 
 PHE   0.024   0.003   PHE C 314 
 TYR   0.015   0.002   TYR C 278 
 ARG   0.004   0.001   ARG C 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04655 (  164)
  hydrogen bonds       : angle       4.49785 (  468)
  covalent geometry    : bond        0.00490 ( 4713)
  covalent geometry    : angle       0.59111 ( 6405)

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 73
  time to evaluate  : 0.485 
Fit side-chains
REVERT: E   63 GLU cc_start: 0.7797 (tp30) cc_final: 0.7580 (mm-30)
REVERT: E  116 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7546 (ptmm)
REVERT: E  312 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7426 (mp0)
REVERT: C   83 GLN cc_start: 0.7554 (mt0) cc_final: 0.7135 (mp10)
REVERT: C  114 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.7798 (m-80)
REVERT: C  233 ARG cc_start: 0.8360 (mtm-85) cc_final: 0.8145 (mtt90)
REVERT: C  272 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7492 (mp0)
  outliers start: 27
  outliers final: 15
  residues processed: 88
  average time/residue: 1.4373
  time to fit residues: 130.5777
Evaluate side-chains
  91 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   57 VAL
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue  116 LYS
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain E residue  223 ASP
Chi-restraints excluded: chain E residue  312 GLU
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue   77 GLU
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  114 PHE
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  162 SER
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  338 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 28 optimal weight:    0.0970
   chunk 2 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   chunk 19 optimal weight:    8.9990
   chunk 50 optimal weight:    0.0050
   chunk 51 optimal weight:    0.9980
   chunk 3 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.8194

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

Flipped N/Q/H residues before XYZ refinement:
E 275 HIS
C 124 GLN
C 148 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.179292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.134689 restraints weight = 4559.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.56
r_work: 0.3129 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.1069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4713  Z= 0.093
  Angle     :  0.478   7.275   6405  Z= 0.235
  Chirality :  0.038   0.146    733
  Planarity :  0.003   0.030    840
  Dihedral  :  6.313  58.057    639
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 25.15 %
    Favored  : 69.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.13 (0.34), residues: 574
  helix:  1.37 (0.36), residues: 220
  sheet:  1.80 (0.57), residues: 84
  loop : -0.06 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E  81 
 HIS   0.001   0.000   HIS E 309 
 PHE   0.018   0.002   PHE C 314 
 TYR   0.010   0.001   TYR E 278 
 ARG   0.003   0.000   ARG E 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03355 (  164)
  hydrogen bonds       : angle       4.25137 (  468)
  covalent geometry    : bond        0.00209 ( 4713)
  covalent geometry    : angle       0.47814 ( 6405)

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 0.545 
Fit side-chains
REVERT: E   63 GLU cc_start: 0.7869 (tp30) cc_final: 0.7667 (mm-30)
REVERT: E  159 LEU cc_start: 0.8014 (mt) cc_final: 0.7746 (mp)
REVERT: E  174 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6755 (mmmt)
REVERT: C   83 GLN cc_start: 0.7479 (mt0) cc_final: 0.7054 (mp10)
REVERT: C  114 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7878 (m-80)
REVERT: C  233 ARG cc_start: 0.8383 (mtm-85) cc_final: 0.8164 (mtt90)
  outliers start: 25
  outliers final: 14
  residues processed: 94
  average time/residue: 1.4425
  time to fit residues: 140.0787
Evaluate side-chains
  89 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue  114 PHE
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain E residue  174 LYS
Chi-restraints excluded: chain E residue  223 ASP
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  114 PHE
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  162 SER
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  198 GLN
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  265 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 15 optimal weight:    7.9990
   chunk 7 optimal weight:   20.0000
   chunk 47 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 56 optimal weight:    0.0870
   chunk 49 optimal weight:    0.8980
   chunk 2 optimal weight:   10.0000
   chunk 13 optimal weight:   20.0000
   overall best weight:    2.3762

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

Flipped N/Q/H residues before XYZ refinement:
E 163 HIS
E 275 HIS
C 148 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.176417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.131971 restraints weight = 4605.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 2.67
r_work: 0.3091 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.1121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4713  Z= 0.146
  Angle     :  0.527   7.477   6405  Z= 0.262
  Chirality :  0.039   0.147    733
  Planarity :  0.004   0.031    840
  Dihedral  :  6.291  56.300    638
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 25.76 %
    Favored  : 69.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.11 (0.34), residues: 574
  helix:  1.39 (0.36), residues: 220
  sheet:  1.89 (0.57), residues: 84
  loop : -0.13 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E  81 
 HIS   0.003   0.001   HIS E 309 
 PHE   0.022   0.002   PHE C 314 
 TYR   0.014   0.002   TYR C 278 
 ARG   0.003   0.000   ARG C 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03922 (  164)
  hydrogen bonds       : angle       4.28449 (  468)
  covalent geometry    : bond        0.00343 ( 4713)
  covalent geometry    : angle       0.52709 ( 6405)

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.513 
Fit side-chains
REVERT: E   63 GLU cc_start: 0.7901 (tp30) cc_final: 0.7687 (mm-30)
REVERT: E  159 LEU cc_start: 0.8068 (mt) cc_final: 0.7793 (mp)
REVERT: E  166 GLU cc_start: 0.6907 (pm20) cc_final: 0.6415 (pm20)
REVERT: C   83 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7120 (mp10)
REVERT: C  114 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.7806 (m-80)
REVERT: C  272 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7517 (mp0)
  outliers start: 23
  outliers final: 14
  residues processed: 90
  average time/residue: 1.4821
  time to fit residues: 137.7086
Evaluate side-chains
  91 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue  114 PHE
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain E residue  223 ASP
Chi-restraints excluded: chain E residue  233 ARG
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  114 PHE
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  162 SER
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  272 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0970
   chunk 51 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   chunk 29 optimal weight:    7.9990
   chunk 3 optimal weight:    8.9990
   chunk 22 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.7582

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

Flipped N/Q/H residues before XYZ refinement:
E 275 HIS
C 148 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.176990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.133781 restraints weight = 4574.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 2.28
r_work: 0.3088 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.1224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4713  Z= 0.120
  Angle     :  0.502   7.179   6405  Z= 0.248
  Chirality :  0.038   0.146    733
  Planarity :  0.003   0.030    840
  Dihedral  :  6.086  56.428    638
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 25.76 %
    Favored  : 69.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.20 (0.34), residues: 574
  helix:  1.48 (0.36), residues: 220
  sheet:  1.84 (0.57), residues: 84
  loop : -0.06 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E  81 
 HIS   0.002   0.001   HIS E 309 
 PHE   0.020   0.002   PHE C 314 
 TYR   0.011   0.001   TYR E 278 
 ARG   0.004   0.000   ARG C 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03570 (  164)
  hydrogen bonds       : angle       4.22099 (  468)
  covalent geometry    : bond        0.00279 ( 4713)
  covalent geometry    : angle       0.50246 ( 6405)

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.525 
Fit side-chains
REVERT: E   63 GLU cc_start: 0.7681 (tp30) cc_final: 0.7478 (mm-30)
REVERT: E  116 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7482 (ptmm)
REVERT: E  159 LEU cc_start: 0.7987 (mt) cc_final: 0.7715 (mp)
REVERT: E  166 GLU cc_start: 0.6876 (pm20) cc_final: 0.6436 (pm20)
REVERT: E  174 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6730 (mmmt)
REVERT: E  233 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.6624 (mtm180)
REVERT: E  300 MET cc_start: 0.7979 (ttm) cc_final: 0.6847 (mpp)
REVERT: C   83 GLN cc_start: 0.7481 (mt0) cc_final: 0.7102 (mp10)
REVERT: C  114 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.7764 (m-80)
REVERT: C  272 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7528 (mp0)
  outliers start: 22
  outliers final: 13
  residues processed: 93
  average time/residue: 1.4181
  time to fit residues: 136.3182
Evaluate side-chains
  91 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue  114 PHE
Chi-restraints excluded: chain E residue  116 LYS
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain E residue  174 LYS
Chi-restraints excluded: chain E residue  223 ASP
Chi-restraints excluded: chain E residue  233 ARG
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  114 PHE
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  162 SER
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  198 GLN
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  272 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 21 optimal weight:    8.9990
   chunk 43 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   chunk 6 optimal weight:    0.2980
   chunk 24 optimal weight:    8.9990
   chunk 50 optimal weight:    0.3980
   chunk 4 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9980
   chunk 1 optimal weight:   20.0000
   overall best weight:    2.5384

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

Flipped N/Q/H residues before XYZ refinement:
E 275 HIS
C 148 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.177499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.134294 restraints weight = 4529.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 2.44
r_work: 0.3082 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.1244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4713  Z= 0.152
  Angle     :  0.532   7.589   6405  Z= 0.263
  Chirality :  0.039   0.146    733
  Planarity :  0.004   0.031    840
  Dihedral  :  5.551  58.527    635
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 24.14 %
    Favored  : 69.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.07 (0.34), residues: 574
  helix:  1.29 (0.36), residues: 220
  sheet:  1.84 (0.57), residues: 84
  loop : -0.08 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E  81 
 HIS   0.003   0.001   HIS E 309 
 PHE   0.022   0.002   PHE C 314 
 TYR   0.013   0.002   TYR C 278 
 ARG   0.002   0.000   ARG C  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03904 (  164)
  hydrogen bonds       : angle       4.27463 (  468)
  covalent geometry    : bond        0.00359 ( 4713)
  covalent geometry    : angle       0.53171 ( 6405)

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 75
  time to evaluate  : 0.539 
Fit side-chains
REVERT: E   63 GLU cc_start: 0.7937 (tp30) cc_final: 0.7717 (mm-30)
REVERT: E  159 LEU cc_start: 0.8060 (mt) cc_final: 0.7776 (mp)
REVERT: E  166 GLU cc_start: 0.6817 (pm20) cc_final: 0.6414 (pm20)
REVERT: E  174 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6766 (mmmt)
REVERT: E  233 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.6597 (mtm180)
REVERT: E  291 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8068 (tm-30)
REVERT: E  300 MET cc_start: 0.8094 (ttm) cc_final: 0.6859 (mpp)
REVERT: C   83 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7114 (mp10)
REVERT: C  109 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8391 (mp0)
REVERT: C  114 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7714 (m-80)
REVERT: C  272 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7568 (mp0)
  outliers start: 29
  outliers final: 12
  residues processed: 93
  average time/residue: 1.4668
  time to fit residues: 140.7426
Evaluate side-chains
  94 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   57 VAL
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue  114 PHE
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain E residue  174 LYS
Chi-restraints excluded: chain E residue  233 ARG
Chi-restraints excluded: chain E residue  291 GLU
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  114 PHE
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  162 SER
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  198 GLN
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  272 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 3 optimal weight:    8.9990
   chunk 52 optimal weight:    1.9990
   chunk 18 optimal weight:   20.0000
   chunk 42 optimal weight:    9.9990
   chunk 27 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 7 optimal weight:   10.0000
   chunk 25 optimal weight:    0.8980
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
E 275 HIS
C 148 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.177616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.135245 restraints weight = 4575.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 2.54
r_work: 0.3075 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.1310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4713  Z= 0.129
  Angle     :  0.516   7.399   6405  Z= 0.253
  Chirality :  0.039   0.146    733
  Planarity :  0.003   0.030    840
  Dihedral  :  5.209  58.433    633
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 24.95 %
    Favored  : 69.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.12 (0.34), residues: 574
  helix:  1.32 (0.36), residues: 220
  sheet:  1.83 (0.57), residues: 84
  loop : -0.02 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E  81 
 HIS   0.003   0.001   HIS E 309 
 PHE   0.021   0.002   PHE C 314 
 TYR   0.011   0.001   TYR C 278 
 ARG   0.002   0.000   ARG C 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03726 (  164)
  hydrogen bonds       : angle       4.23936 (  468)
  covalent geometry    : bond        0.00304 ( 4713)
  covalent geometry    : angle       0.51561 ( 6405)

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 76
  time to evaluate  : 0.692 
Fit side-chains
REVERT: E   63 GLU cc_start: 0.7713 (tp30) cc_final: 0.7503 (mm-30)
REVERT: E  159 LEU cc_start: 0.8002 (mt) cc_final: 0.7729 (mp)
REVERT: E  166 GLU cc_start: 0.6816 (pm20) cc_final: 0.6440 (pm20)
REVERT: E  174 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6733 (mmmt)
REVERT: E  233 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6599 (mtm180)
REVERT: E  291 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7960 (tm-30)
REVERT: E  300 MET cc_start: 0.7990 (ttm) cc_final: 0.6878 (mpp)
REVERT: C   83 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7110 (mp10)
REVERT: C  109 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8161 (mp0)
REVERT: C  112 ARG cc_start: 0.8179 (ttp-110) cc_final: 0.7903 (ttm-80)
REVERT: C  114 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.7665 (m-80)
REVERT: C  272 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7553 (mp0)
  outliers start: 25
  outliers final: 13
  residues processed: 91
  average time/residue: 1.4908
  time to fit residues: 140.1136
Evaluate side-chains
  93 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   57 VAL
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue  114 PHE
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain E residue  174 LYS
Chi-restraints excluded: chain E residue  223 ASP
Chi-restraints excluded: chain E residue  233 ARG
Chi-restraints excluded: chain E residue  291 GLU
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  114 PHE
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  162 SER
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  198 GLN
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  272 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 24 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 11 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 25 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 9 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
E 275 HIS
C 148 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.176609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.134270 restraints weight = 4706.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.62
r_work: 0.3064 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.1339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4713  Z= 0.169
  Angle     :  0.546   8.054   6405  Z= 0.270
  Chirality :  0.040   0.144    733
  Planarity :  0.004   0.031    840
  Dihedral  :  5.362  59.626    633
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 25.96 %
    Favored  : 69.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.00 (0.34), residues: 574
  helix:  1.17 (0.35), residues: 220
  sheet:  1.86 (0.57), residues: 84
  loop : -0.08 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP E  81 
 HIS   0.003   0.001   HIS E 309 
 PHE   0.022   0.002   PHE C 314 
 TYR   0.013   0.002   TYR C 278 
 ARG   0.003   0.000   ARG C  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04104 (  164)
  hydrogen bonds       : angle       4.32504 (  468)
  covalent geometry    : bond        0.00401 ( 4713)
  covalent geometry    : angle       0.54620 ( 6405)

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.533 
Fit side-chains
REVERT: E   63 GLU cc_start: 0.7701 (tp30) cc_final: 0.7497 (mm-30)
REVERT: E  116 LYS cc_start: 0.7554 (ptmm) cc_final: 0.7328 (ptmm)
REVERT: E  159 LEU cc_start: 0.8046 (mt) cc_final: 0.7772 (mp)
REVERT: E  166 GLU cc_start: 0.6761 (pm20) cc_final: 0.6362 (pm20)
REVERT: E  174 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6748 (mmmt)
REVERT: E  233 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.6632 (mtm180)
REVERT: E  300 MET cc_start: 0.8023 (ttm) cc_final: 0.6915 (mpp)
REVERT: C   83 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7096 (mp10)
REVERT: C  109 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8217 (mp0)
REVERT: C  114 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.7663 (m-80)
REVERT: C  272 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7642 (mp0)
  outliers start: 22
  outliers final: 12
  residues processed: 87
  average time/residue: 1.4423
  time to fit residues: 129.6375
Evaluate side-chains
  94 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   57 VAL
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain E residue  174 LYS
Chi-restraints excluded: chain E residue  233 ARG
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  114 PHE
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  162 SER
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  198 GLN
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  272 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 44 optimal weight:    8.9990
   chunk 22 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0470
   chunk 40 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   chunk 2 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.8480

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

Flipped N/Q/H residues before XYZ refinement:
E 275 HIS
C 124 GLN
C 148 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.179643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.136462 restraints weight = 4569.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.41
r_work: 0.3122 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4713  Z= 0.092
  Angle     :  0.485   7.186   6405  Z= 0.235
  Chirality :  0.038   0.145    733
  Planarity :  0.003   0.031    840
  Dihedral  :  5.044  57.231    633
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 26.98 %
    Favored  : 69.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.20 (0.35), residues: 574
  helix:  1.42 (0.36), residues: 221
  sheet:  1.77 (0.57), residues: 84
  loop :  0.02 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E  81 
 HIS   0.002   0.001   HIS E 309 
 PHE   0.018   0.002   PHE C 314 
 TYR   0.008   0.001   TYR C 278 
 ARG   0.003   0.000   ARG E 246 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03248 (  164)
  hydrogen bonds       : angle       4.16329 (  468)
  covalent geometry    : bond        0.00215 ( 4713)
  covalent geometry    : angle       0.48452 ( 6405)

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

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

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1148 Ramachandran restraints generated.
    574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.528 
Fit side-chains
REVERT: E   63 GLU cc_start: 0.7680 (tp30) cc_final: 0.7458 (mm-30)
REVERT: E  116 LYS cc_start: 0.7509 (ptmm) cc_final: 0.7297 (ptmm)
REVERT: E  159 LEU cc_start: 0.7987 (mt) cc_final: 0.7706 (mp)
REVERT: E  166 GLU cc_start: 0.6799 (pm20) cc_final: 0.6325 (pm20)
REVERT: E  174 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6707 (mmmt)
REVERT: E  233 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.6581 (mtm180)
REVERT: E  291 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7973 (tm-30)
REVERT: E  300 MET cc_start: 0.7911 (ttm) cc_final: 0.6833 (mpp)
REVERT: C   83 GLN cc_start: 0.7454 (mt0) cc_final: 0.7009 (mp10)
REVERT: C  109 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8332 (mm-30)
REVERT: C  112 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7715 (ttm-80)
REVERT: C  114 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.7741 (m-80)
REVERT: C  272 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7581 (mp0)
  outliers start: 19
  outliers final: 8
  residues processed: 90
  average time/residue: 1.5475
  time to fit residues: 143.6444
Evaluate side-chains
  92 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   65 VAL
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain E residue  174 LYS
Chi-restraints excluded: chain E residue  233 ARG
Chi-restraints excluded: chain E residue  291 GLU
Chi-restraints excluded: chain C residue   72 GLU
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  109 GLU
Chi-restraints excluded: chain C residue  114 PHE
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  198 GLN
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  272 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 56 optimal weight:    0.3980
   chunk 32 optimal weight:   10.0000
   chunk 17 optimal weight:    0.3980
   chunk 54 optimal weight:   10.0000
   chunk 51 optimal weight:    8.9990
   chunk 53 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 9 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 25 optimal weight:    0.1980
   overall best weight:    2.7984

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

Flipped N/Q/H residues before XYZ refinement:
E 275 HIS
C 148 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.177042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.132889 restraints weight = 4584.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 2.23
r_work: 0.3115 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4713  Z= 0.164
  Angle     :  0.546   7.587   6405  Z= 0.269
  Chirality :  0.040   0.144    733
  Planarity :  0.004   0.031    840
  Dihedral  :  5.274  59.646    633
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 26.98 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.06 (0.34), residues: 574
  helix:  1.26 (0.36), residues: 220
  sheet:  1.82 (0.56), residues: 84
  loop : -0.06 (0.35), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E  81 
 HIS   0.003   0.001   HIS E 309 
 PHE   0.022   0.002   PHE C 314 
 TYR   0.013   0.002   TYR C 278 
 ARG   0.002   0.000   ARG C  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03981 (  164)
  hydrogen bonds       : angle       4.25050 (  468)
  covalent geometry    : bond        0.00392 ( 4713)
  covalent geometry    : angle       0.54619 ( 6405)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5064.62 seconds
wall clock time: 87 minutes 2.20 seconds (5222.20 seconds total)