Starting phenix.real_space_refine
on Tue Feb 11 06:42:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8csy_26975/02_2025/8csy_26975.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8csy_26975/02_2025/8csy_26975.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/8csy_26975/02_2025/8csy_26975.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8csy_26975/02_2025/8csy_26975.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8csy_26975/02_2025/8csy_26975.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8csy_26975/02_2025/8csy_26975.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=   0.291
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     880      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4638
  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: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "C"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
  Time building chain proxies: 3.54, per 1000 atoms: 0.76
  Number of scatterers: 4638
  At special positions: 0
  Unit cell: (89.64, 83, 74.285, 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     880      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: 1.04
  Conformation dependent library (CDL) restraints added in 624.4 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:
      22 helices and 4 sheets defined
      40.1% alpha, 12.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'E' and resid 104 through 116
      removed outlier: 3.834A  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 301
    Processing helix  chain 'E' and resid 303 through 317
      removed outlier: 3.730A  pdb=" N   LEU E 307 " --> pdb=" O   SER E 303 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 328 through 333
    Processing helix  chain 'E' and resid 335 through 348
    Processing helix  chain 'C' and resid 42 through 47
      removed outlier: 3.532A  pdb=" N   HIS C  47 " --> pdb=" O   THR C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 116
      removed outlier: 3.688A  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 149 through 158
    Processing helix  chain 'C' and resid 163 through 167
    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: 3.689A  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: 4.268A  pdb=" N   VAL C 338 " --> pdb=" O   SER C 334 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 58 through 67
      removed outlier: 6.017A  pdb=" N   GLU E  63 " --> pdb=" O   GLU E  77 " (cutoff:3.500A)
      removed outlier: 5.572A  pdb=" N   GLU E  77 " --> pdb=" O   GLU E  63 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   VAL E  65 " --> pdb=" O   TRP E  75 " (cutoff:3.500A)
      removed outlier: 4.865A  pdb=" N   TRP E  75 " --> pdb=" O   VAL E  65 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ASP E  67 " --> pdb=" O   LEU E  73 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   LEU E  73 " --> pdb=" O   ASP E  67 " (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 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 'E' and resid 177 through 178
    Processing sheet with id=AA4, first strand: chain 'C' and resid 56 through 66
      removed outlier: 6.584A  pdb=" N   VAL C  59 " --> pdb=" O   ARG C  80 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   ARG C  80 " --> pdb=" O   VAL C  59 " (cutoff:3.500A)
      removed outlier: 6.689A  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

    165 hydrogen bonds defined for protein.
    465 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: 1.12

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1575
        1.34 -     1.46: 781
        1.46 -     1.57: 2337
        1.57 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 4713
  Sorted by residual:
  bond pdb=" C   VAL E 336 "
       pdb=" N   PRO E 337 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.011 1.28e-02 6.10e+03 7.71e-01
  bond pdb=" C   VAL C 336 "
       pdb=" N   PRO C 337 "
    ideal  model  delta    sigma   weight residual
    1.336  1.346 -0.011 1.23e-02 6.61e+03 7.66e-01
  bond pdb=" C   PRO C 221 "
       pdb=" N   PRO C 222 "
    ideal  model  delta    sigma   weight residual
    1.335  1.344 -0.009 1.30e-02 5.92e+03 4.91e-01
  bond pdb=" CA  PRO C 271 "
       pdb=" C   PRO C 271 "
    ideal  model  delta    sigma   weight residual
    1.525  1.519  0.007 9.70e-03 1.06e+04 4.61e-01
  bond pdb=" N   ASP E 122 "
       pdb=" CA  ASP E 122 "
    ideal  model  delta    sigma   weight residual
    1.460  1.469 -0.010 1.42e-02 4.96e+03 4.56e-01
  ... (remaining 4708 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.36: 6213
        1.36 -     2.71: 155
        2.71 -     4.07: 27
        4.07 -     5.42: 6
        5.42 -     6.78: 4
  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  108.87    5.22 1.55e+00 4.16e-01 1.13e+01
  angle pdb=" C   VAL E  82 "
        pdb=" N   GLN E  83 "
        pdb=" CA  GLN E  83 "
      ideal   model   delta    sigma   weight residual
     121.54  127.29   -5.75 1.91e+00 2.74e-01 9.06e+00
  angle pdb=" N   GLU C  90 "
        pdb=" CA  GLU C  90 "
        pdb=" C   GLU C  90 "
      ideal   model   delta    sigma   weight residual
     111.81  108.25    3.56 1.44e+00 4.82e-01 6.10e+00
  angle pdb=" N   VAL E  82 "
        pdb=" CA  VAL E  82 "
        pdb=" C   VAL E  82 "
      ideal   model   delta    sigma   weight residual
     109.34  104.62    4.72 2.08e+00 2.31e-01 5.15e+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  116.96   -2.22 1.03e+00 9.43e-01 4.64e+00
  ... (remaining 6400 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.74: 2624
       16.74 -    33.47: 149
       33.47 -    50.21: 70
       50.21 -    66.94: 23
       66.94 -    83.68: 5
  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  155.74   24.26     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" CA  VAL C  57 "
           pdb=" C   VAL C  57 "
           pdb=" N   TYR C  58 "
           pdb=" CA  TYR C  58 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.18   17.82     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CB  GLU E 312 "
           pdb=" CG  GLU E 312 "
           pdb=" CD  GLU E 312 "
           pdb=" OE1 GLU E 312 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   83.68  -83.68     1      3.00e+01 1.11e-03 9.49e+00
  ... (remaining 2868 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 441
       0.029 -    0.057: 187
       0.057 -    0.085: 71
       0.085 -    0.114: 31
       0.114 -    0.142: 3
  Chirality restraints: 733
  Sorted by residual:
  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    2.58   -0.14 2.00e-01 2.50e+01 5.07e-01
  chirality pdb=" CA  ILE E 220 "
            pdb=" N   ILE E 220 "
            pdb=" C   ILE E 220 "
            pdb=" CB  ILE E 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.50e-01
  chirality pdb=" CA  VAL C  82 "
            pdb=" N   VAL C  82 "
            pdb=" C   VAL C  82 "
            pdb=" CB  VAL C  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.11 2.00e-01 2.50e+01 3.28e-01
  ... (remaining 730 not shown)

  Planarity restraints: 840
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 146 "   -0.025 5.00e-02 4.00e+02   3.81e-02 2.32e+00
        pdb=" N   PRO C 147 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO C 147 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C 147 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 183 "   -0.023 5.00e-02 4.00e+02   3.49e-02 1.94e+00
        pdb=" N   PRO E 184 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO E 184 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO E 184 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E 146 "   -0.021 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO E 147 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO E 147 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO E 147 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 837 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 688
        2.76 -     3.29: 4203
        3.29 -     3.83: 8186
        3.83 -     4.36: 9643
        4.36 -     4.90: 16030
  Nonbonded interactions: 38750
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 103 "
            pdb=" OG  SER C 106 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" NH2 ARG E 292 "
            pdb=" O   LYS E 353 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" OD1 ASP E 316 "
            pdb=" NE1 TRP C 105 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" O   ALA E 331 "
            pdb=" OG  SER E 334 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OD2 ASP C 122 "
            pdb=" O   HOH C1001 "
     model   vdw
     2.328 3.040
  ... (remaining 38745 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:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     15.150
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
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      :  0.003   0.033   4713  Z= 0.195
  Angle     :  0.559   6.781   6405  Z= 0.303
  Chirality :  0.038   0.142    733
  Planarity :  0.005   0.038    840
  Dihedral  : 14.356  83.678   1763
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  :  8.72 %
    Favored  : 87.22 %
  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:  1.13 (0.36), residues: 212
  sheet:  2.27 (0.52), residues: 89
  loop : -0.10 (0.35), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  81 
 HIS   0.003   0.001   HIS E 101 
 PHE   0.020   0.002   PHE C 314 
 TYR   0.009   0.001   TYR E 278 
 ARG   0.003   0.000   ARG E 304 

*********************** 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
  128 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   69 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.5567 (ptpt)
REVERT: E  112 ARG cc_start: 0.7610 (ttm-80) cc_final: 0.7350 (ttp-170)
REVERT: E  125 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7840 (mm-30)
REVERT: E  233 ARG cc_start: 0.8376 (mtm180) cc_final: 0.8161 (mtm180)
REVERT: E  291 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8683 (tm-30)
REVERT: E  348 GLN cc_start: 0.7370 (pt0) cc_final: 0.7159 (pt0)
REVERT: C   83 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7345 (pm20)
REVERT: C  109 GLU cc_start: 0.7684 (tp30) cc_final: 0.7363 (mp0)
REVERT: C  124 GLN cc_start: 0.8431 (mt0) cc_final: 0.7772 (tm-30)
REVERT: C  198 GLN cc_start: 0.7841 (tt0) cc_final: 0.7400 (mt0)
REVERT: C  300 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7721 (mmm)
  outliers start: 20
  outliers final: 3
  residues processed: 123
  average time/residue: 1.6194
  time to fit residues: 205.4890
Evaluate side-chains
  103 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   69 LYS
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  291 GLU
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  300 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 43 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 44 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 28 optimal weight:    9.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
C  83 GLN
C 144 GLN
C 239 GLN
C 248 GLN
C 339 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.146947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.117589 restraints weight = 4957.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 1.84
r_work: 0.3026 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   4713  Z= 0.303
  Angle     :  0.597   6.405   6405  Z= 0.301
  Chirality :  0.041   0.126    733
  Planarity :  0.005   0.036    840
  Dihedral  :  7.153  59.298    647
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 11.97 %
    Favored  : 83.16 %
  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:  1.03 (0.34), residues: 574
  helix:  1.27 (0.36), residues: 218
  sheet:  2.22 (0.56), residues: 78
  loop : -0.20 (0.34), residues: 278

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   0.023   0.002   PHE C 314 
 TYR   0.011   0.002   TYR E 278 
 ARG   0.004   0.001   ARG E 304 

*********************** 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
  115 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
REVERT: E   69 LYS cc_start: 0.6745 (OUTLIER) cc_final: 0.5814 (ptpt)
REVERT: E  112 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7338 (ttp-170)
REVERT: E  116 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8081 (ptmt)
REVERT: E  125 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7874 (mm-30)
REVERT: E  198 GLN cc_start: 0.6979 (mt0) cc_final: 0.6277 (tp40)
REVERT: E  219 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.5646 (pmtt)
REVERT: E  239 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7807 (pm20)
REVERT: E  348 GLN cc_start: 0.7689 (pt0) cc_final: 0.7343 (pt0)
REVERT: C   83 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7558 (pm20)
REVERT: C  109 GLU cc_start: 0.7884 (tp30) cc_final: 0.7388 (mm-30)
REVERT: C  114 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7831 (t80)
REVERT: C  124 GLN cc_start: 0.8723 (mt0) cc_final: 0.7817 (tm-30)
REVERT: C  155 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7941 (ttp-110)
REVERT: C  202 GLU cc_start: 0.4389 (OUTLIER) cc_final: 0.3796 (tp30)
REVERT: C  233 ARG cc_start: 0.8250 (mtt-85) cc_final: 0.7955 (mpp80)
REVERT: C  272 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7189 (mm-30)
REVERT: C  300 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8001 (mmm)
REVERT: C  330 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7324 (tt0)
  outliers start: 24
  outliers final: 7
  residues processed: 103
  average time/residue: 1.4643
  time to fit residues: 155.6062
Evaluate side-chains
  99 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   69 LYS
Chi-restraints excluded: chain E residue   84 LEU
Chi-restraints excluded: chain E residue  116 LYS
Chi-restraints excluded: chain E residue  158 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  219 LYS
Chi-restraints excluded: chain E residue  239 GLN
Chi-restraints excluded: chain E residue  260 VAL
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue  114 PHE
Chi-restraints excluded: chain C residue  155 ARG
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  300 MET
Chi-restraints excluded: chain C residue  330 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 55 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 15 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 41 optimal weight:    7.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
C 239 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.145287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.115702 restraints weight = 4968.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 1.83
r_work: 0.3003 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2861 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   4713  Z= 0.385
  Angle     :  0.646   7.120   6405  Z= 0.325
  Chirality :  0.044   0.123    733
  Planarity :  0.005   0.039    840
  Dihedral  :  6.812  53.087    644
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 12.58 %
    Favored  : 81.54 %
  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:  0.61 (0.33), residues: 574
  helix:  1.01 (0.36), residues: 219
  sheet:  1.91 (0.55), residues: 78
  loop : -0.50 (0.33), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E  81 
 HIS   0.005   0.001   HIS C 163 
 PHE   0.025   0.003   PHE C 314 
 TYR   0.012   0.003   TYR C 278 
 ARG   0.005   0.001   ARG E 304 

*********************** 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
  118 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 89
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
REVERT: E   69 LYS cc_start: 0.6850 (OUTLIER) cc_final: 0.5906 (ptpt)
REVERT: E   83 GLN cc_start: 0.8340 (tp-100) cc_final: 0.8003 (mm-40)
REVERT: E  112 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7351 (ttp-170)
REVERT: E  116 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8063 (ptmt)
REVERT: E  125 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7864 (mm-30)
REVERT: E  198 GLN cc_start: 0.7011 (mt0) cc_final: 0.6298 (tp40)
REVERT: E  219 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.5660 (pmtt)
REVERT: E  239 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7924 (pm20)
REVERT: E  348 GLN cc_start: 0.7760 (pt0) cc_final: 0.7377 (pt0)
REVERT: C   83 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7596 (pm20)
REVERT: C  109 GLU cc_start: 0.7927 (tp30) cc_final: 0.7542 (mm-30)
REVERT: C  114 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7837 (t80)
REVERT: C  124 GLN cc_start: 0.8706 (mt0) cc_final: 0.7805 (tm-30)
REVERT: C  155 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7939 (ttp-110)
REVERT: C  202 GLU cc_start: 0.4488 (OUTLIER) cc_final: 0.3918 (tp30)
REVERT: C  216 ILE cc_start: 0.5884 (OUTLIER) cc_final: 0.5316 (tp)
REVERT: C  252 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7962 (mt-10)
REVERT: C  272 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7278 (mm-30)
REVERT: C  300 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8012 (mmm)
REVERT: C  330 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7365 (tt0)
  outliers start: 29
  outliers final: 7
  residues processed: 105
  average time/residue: 1.3930
  time to fit residues: 151.2240
Evaluate side-chains
  100 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   69 LYS
Chi-restraints excluded: chain E residue   84 LEU
Chi-restraints excluded: chain E residue  116 LYS
Chi-restraints excluded: chain E residue  158 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  219 LYS
Chi-restraints excluded: chain E residue  239 GLN
Chi-restraints excluded: chain E residue  260 VAL
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue  114 PHE
Chi-restraints excluded: chain C residue  155 ARG
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  216 ILE
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  300 MET
Chi-restraints excluded: chain C residue  330 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 0 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 55 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
C 239 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.145991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.116615 restraints weight = 4905.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 1.81
r_work: 0.3001 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2853 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   4713  Z= 0.315
  Angle     :  0.593   6.728   6405  Z= 0.300
  Chirality :  0.041   0.120    733
  Planarity :  0.005   0.037    840
  Dihedral  :  6.686  52.697    644
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 14.40 %
    Favored  : 80.53 %
  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:  0.63 (0.33), residues: 574
  helix:  1.07 (0.36), residues: 218
  sheet:  1.83 (0.55), residues: 78
  loop : -0.50 (0.33), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E  81 
 HIS   0.005   0.001   HIS C 163 
 PHE   0.024   0.003   PHE C 314 
 TYR   0.012   0.002   TYR C 278 
 ARG   0.006   0.001   ARG E 138 

*********************** 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
  108 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 0.498 
Fit side-chains
   revert: symmetry clash
REVERT: E   60 GLU cc_start: 0.8898 (tt0) cc_final: 0.8688 (tt0)
REVERT: E   69 LYS cc_start: 0.6852 (OUTLIER) cc_final: 0.5875 (ptpt)
REVERT: E   83 GLN cc_start: 0.8284 (tp-100) cc_final: 0.7976 (mm-40)
REVERT: E  112 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7319 (ttp-170)
REVERT: E  125 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7937 (mm-30)
REVERT: E  198 GLN cc_start: 0.6990 (mt0) cc_final: 0.6397 (tp-100)
REVERT: E  219 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.5618 (pmtt)
REVERT: E  239 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7797 (pm20)
REVERT: E  348 GLN cc_start: 0.7736 (pt0) cc_final: 0.7335 (pt0)
REVERT: C   83 GLN cc_start: 0.7988 (pt0) cc_final: 0.7619 (pm20)
REVERT: C  109 GLU cc_start: 0.7912 (tp30) cc_final: 0.7511 (mm-30)
REVERT: C  114 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7832 (t80)
REVERT: C  124 GLN cc_start: 0.8759 (mt0) cc_final: 0.7792 (tm-30)
REVERT: C  155 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7957 (ttp-110)
REVERT: C  202 GLU cc_start: 0.4489 (OUTLIER) cc_final: 0.3909 (tp30)
REVERT: C  216 ILE cc_start: 0.5877 (OUTLIER) cc_final: 0.5293 (tp)
REVERT: C  252 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7970 (mt-10)
REVERT: C  272 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7308 (mm-30)
REVERT: C  300 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8023 (mmm)
REVERT: C  330 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7325 (tt0)
  outliers start: 25
  outliers final: 7
  residues processed: 97
  average time/residue: 1.5007
  time to fit residues: 150.4019
Evaluate side-chains
  101 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   69 LYS
Chi-restraints excluded: chain E residue   84 LEU
Chi-restraints excluded: chain E residue  158 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  219 LYS
Chi-restraints excluded: chain E residue  239 GLN
Chi-restraints excluded: chain E residue  260 VAL
Chi-restraints excluded: chain C residue  114 PHE
Chi-restraints excluded: chain C residue  155 ARG
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  216 ILE
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  260 VAL
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  300 MET
Chi-restraints excluded: chain C residue  330 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 50 optimal weight:    0.6980
   chunk 55 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 43 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 44 optimal weight:    8.9990
   chunk 34 optimal weight:    8.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
E 134 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.148146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.118874 restraints weight = 4983.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 1.83
r_work: 0.3054 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4713  Z= 0.171
  Angle     :  0.500   6.004   6405  Z= 0.253
  Chirality :  0.038   0.119    733
  Planarity :  0.004   0.035    840
  Dihedral  :  6.196  52.722    641
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 15.01 %
    Favored  : 80.32 %
  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:  0.96 (0.34), residues: 574
  helix:  1.33 (0.37), residues: 218
  sheet:  1.91 (0.57), residues: 78
  loop : -0.27 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E  81 
 HIS   0.003   0.001   HIS C 101 
 PHE   0.019   0.002   PHE C 314 
 TYR   0.010   0.001   TYR E 278 
 ARG   0.007   0.000   ARG E 138 

*********************** 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
  110 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
REVERT: E   69 LYS cc_start: 0.6846 (OUTLIER) cc_final: 0.5804 (ptpt)
REVERT: E   83 GLN cc_start: 0.8068 (tp-100) cc_final: 0.7798 (mm-40)
REVERT: E  112 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7349 (ttp-170)
REVERT: E  125 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7903 (mm-30)
REVERT: E  158 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8348 (mm)
REVERT: E  219 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.5565 (pmtt)
REVERT: E  348 GLN cc_start: 0.7602 (pt0) cc_final: 0.7187 (pt0)
REVERT: C   83 GLN cc_start: 0.7871 (pt0) cc_final: 0.7523 (pm20)
REVERT: C  109 GLU cc_start: 0.7865 (tp30) cc_final: 0.7402 (mm-30)
REVERT: C  114 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7894 (t80)
REVERT: C  124 GLN cc_start: 0.8729 (mt0) cc_final: 0.7833 (tm-30)
REVERT: C  202 GLU cc_start: 0.4372 (OUTLIER) cc_final: 0.3825 (tp30)
REVERT: C  216 ILE cc_start: 0.5779 (OUTLIER) cc_final: 0.5197 (tp)
REVERT: C  252 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7969 (mt-10)
REVERT: C  272 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7226 (mm-30)
REVERT: C  300 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7958 (mmm)
REVERT: C  328 SER cc_start: 0.7956 (m) cc_final: 0.7660 (t)
REVERT: C  330 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7316 (tt0)
  outliers start: 23
  outliers final: 5
  residues processed: 100
  average time/residue: 1.3897
  time to fit residues: 143.6467
Evaluate side-chains
  101 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   69 LYS
Chi-restraints excluded: chain E residue  158 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  219 LYS
Chi-restraints excluded: chain E residue  260 VAL
Chi-restraints excluded: chain C residue  114 PHE
Chi-restraints excluded: chain C residue  116 LYS
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  216 ILE
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  300 MET
Chi-restraints excluded: chain C residue  330 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 32 optimal weight:    9.9990
   chunk 55 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 43 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
C 239 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.146727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.117353 restraints weight = 4939.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.83
r_work: 0.3036 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4713  Z= 0.261
  Angle     :  0.554   6.171   6405  Z= 0.279
  Chirality :  0.040   0.120    733
  Planarity :  0.004   0.035    840
  Dihedral  :  6.304  52.310    641
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 16.43 %
    Favored  : 79.31 %
  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:  0.87 (0.34), residues: 574
  helix:  1.30 (0.37), residues: 218
  sheet:  1.83 (0.57), residues: 78
  loop : -0.33 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP E  81 
 HIS   0.004   0.001   HIS C 163 
 PHE   0.022   0.002   PHE C 314 
 TYR   0.011   0.002   TYR C 278 
 ARG   0.006   0.000   ARG E 138 

*********************** 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
  106 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
REVERT: E   69 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.5862 (ptpt)
REVERT: E   83 GLN cc_start: 0.8112 (tp-100) cc_final: 0.7850 (mm-40)
REVERT: E  112 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7365 (ttp-170)
REVERT: E  125 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7926 (mm-30)
REVERT: E  158 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8410 (mm)
REVERT: E  198 GLN cc_start: 0.6925 (mt0) cc_final: 0.6255 (tp40)
REVERT: E  219 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.5654 (pmtt)
REVERT: E  348 GLN cc_start: 0.7646 (pt0) cc_final: 0.7217 (pt0)
REVERT: C   83 GLN cc_start: 0.7916 (pt0) cc_final: 0.7562 (pm20)
REVERT: C  109 GLU cc_start: 0.7887 (tp30) cc_final: 0.7463 (mm-30)
REVERT: C  114 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7913 (t80)
REVERT: C  124 GLN cc_start: 0.8691 (mt0) cc_final: 0.7802 (tm-30)
REVERT: C  202 GLU cc_start: 0.4454 (OUTLIER) cc_final: 0.3917 (tp30)
REVERT: C  216 ILE cc_start: 0.5853 (OUTLIER) cc_final: 0.5278 (tp)
REVERT: C  233 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7184 (mtt-85)
REVERT: C  252 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7998 (mt-10)
REVERT: C  272 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7313 (mm-30)
REVERT: C  300 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7970 (mmm)
REVERT: C  330 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7350 (tt0)
  outliers start: 21
  outliers final: 5
  residues processed: 97
  average time/residue: 1.3781
  time to fit residues: 138.2588
Evaluate side-chains
  96 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   69 LYS
Chi-restraints excluded: chain E residue  158 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  174 LYS
Chi-restraints excluded: chain E residue  219 LYS
Chi-restraints excluded: chain E residue  260 VAL
Chi-restraints excluded: chain C residue  114 PHE
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  216 ILE
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 ARG
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  300 MET
Chi-restraints excluded: chain C residue  330 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 42 optimal weight:    0.2980
   chunk 29 optimal weight:    9.9990
   chunk 50 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 13 optimal weight:   50.0000
   chunk 52 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    3.2588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.146118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.116862 restraints weight = 4893.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.82
r_work: 0.3031 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4713  Z= 0.280
  Angle     :  0.569   6.268   6405  Z= 0.287
  Chirality :  0.040   0.119    733
  Planarity :  0.004   0.035    840
  Dihedral  :  6.386  53.007    641
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 16.02 %
    Favored  : 78.90 %
  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:  0.77 (0.34), residues: 574
  helix:  1.24 (0.37), residues: 218
  sheet:  1.67 (0.57), residues: 78
  loop : -0.38 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP E  81 
 HIS   0.005   0.001   HIS C 163 
 PHE   0.022   0.002   PHE C 314 
 TYR   0.011   0.002   TYR C 278 
 ARG   0.006   0.001   ARG E 138 

*********************** 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
  108 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
REVERT: E   69 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.5890 (ptpt)
REVERT: E   83 GLN cc_start: 0.8113 (tp-100) cc_final: 0.7841 (mm-40)
REVERT: E  112 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7355 (ttp-170)
REVERT: E  125 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7924 (mm-30)
REVERT: E  198 GLN cc_start: 0.6968 (mt0) cc_final: 0.6412 (tp-100)
REVERT: E  219 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.5676 (pmtt)
REVERT: E  348 GLN cc_start: 0.7670 (pt0) cc_final: 0.7248 (pt0)
REVERT: C  109 GLU cc_start: 0.7895 (tp30) cc_final: 0.7407 (mm-30)
REVERT: C  114 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.7838 (t80)
REVERT: C  124 GLN cc_start: 0.8709 (mt0) cc_final: 0.7802 (tm-30)
REVERT: C  202 GLU cc_start: 0.4462 (OUTLIER) cc_final: 0.3917 (tp30)
REVERT: C  216 ILE cc_start: 0.5839 (OUTLIER) cc_final: 0.5259 (tp)
REVERT: C  233 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7243 (mtt-85)
REVERT: C  252 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8003 (mt-10)
REVERT: C  300 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7966 (mmm)
REVERT: C  330 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7359 (tt0)
  outliers start: 25
  outliers final: 9
  residues processed: 98
  average time/residue: 1.4382
  time to fit residues: 145.5138
Evaluate side-chains
  100 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   69 LYS
Chi-restraints excluded: chain E residue  158 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  174 LYS
Chi-restraints excluded: chain E residue  219 LYS
Chi-restraints excluded: chain E residue  260 VAL
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue  114 PHE
Chi-restraints excluded: chain C residue  153 LEU
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  216 ILE
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 ARG
Chi-restraints excluded: chain C residue  300 MET
Chi-restraints excluded: chain C residue  330 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 28 optimal weight:    0.0020
   chunk 46 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 43 optimal weight:    9.9990
   chunk 22 optimal weight:    6.9990
   chunk 0 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   overall best weight:    2.3996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.147150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.117751 restraints weight = 4938.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.84
r_work: 0.3044 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.1841

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= 0.221
  Angle     :  0.532   6.058   6405  Z= 0.268
  Chirality :  0.039   0.118    733
  Planarity :  0.004   0.034    840
  Dihedral  :  6.272  52.593    641
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 17.24 %
    Favored  : 79.11 %
  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:  0.86 (0.34), residues: 574
  helix:  1.31 (0.37), residues: 218
  sheet:  1.65 (0.57), residues: 78
  loop : -0.30 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP E  81 
 HIS   0.003   0.001   HIS C 101 
 PHE   0.021   0.002   PHE C 314 
 TYR   0.009   0.002   TYR E 278 
 ARG   0.007   0.000   ARG E 138 

*********************** 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
  106 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
REVERT: E   69 LYS cc_start: 0.6873 (OUTLIER) cc_final: 0.5882 (ptpt)
REVERT: E   83 GLN cc_start: 0.8070 (tp-100) cc_final: 0.7805 (mm-40)
REVERT: E  112 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7354 (ttp-170)
REVERT: E  125 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7928 (mm-30)
REVERT: E  158 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8397 (mm)
REVERT: E  219 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.5650 (pmtt)
REVERT: E  291 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7946 (tm-30)
REVERT: E  348 GLN cc_start: 0.7626 (pt0) cc_final: 0.7203 (pt0)
REVERT: C   83 GLN cc_start: 0.7910 (pt0) cc_final: 0.7698 (pm20)
REVERT: C  109 GLU cc_start: 0.7901 (tp30) cc_final: 0.7331 (mm-30)
REVERT: C  114 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7901 (t80)
REVERT: C  124 GLN cc_start: 0.8706 (mt0) cc_final: 0.7797 (tm-30)
REVERT: C  202 GLU cc_start: 0.4447 (OUTLIER) cc_final: 0.3927 (tp30)
REVERT: C  216 ILE cc_start: 0.5800 (OUTLIER) cc_final: 0.5198 (tp)
REVERT: C  233 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7240 (mtt-85)
REVERT: C  252 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7998 (mt-10)
REVERT: C  300 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7967 (mmm)
REVERT: C  330 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7352 (tt0)
  outliers start: 18
  outliers final: 6
  residues processed: 99
  average time/residue: 1.4068
  time to fit residues: 143.9202
Evaluate side-chains
  98 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   69 LYS
Chi-restraints excluded: chain E residue  158 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  174 LYS
Chi-restraints excluded: chain E residue  219 LYS
Chi-restraints excluded: chain E residue  260 VAL
Chi-restraints excluded: chain E residue  291 GLU
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue  114 PHE
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  216 ILE
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 ARG
Chi-restraints excluded: chain C residue  300 MET
Chi-restraints excluded: chain C residue  330 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 4 optimal weight:    4.9990
   chunk 43 optimal weight:   10.0000
   chunk 50 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
C  71 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.146732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.117277 restraints weight = 4976.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 1.84
r_work: 0.3041 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4713  Z= 0.251
  Angle     :  0.552   6.104   6405  Z= 0.278
  Chirality :  0.040   0.119    733
  Planarity :  0.004   0.034    840
  Dihedral  :  6.314  52.882    641
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 17.44 %
    Favored  : 78.50 %
  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:  0.82 (0.34), residues: 574
  helix:  1.29 (0.37), residues: 218
  sheet:  1.60 (0.56), residues: 78
  loop : -0.33 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP E  81 
 HIS   0.004   0.001   HIS C 163 
 PHE   0.021   0.002   PHE C 314 
 TYR   0.010   0.002   TYR C 278 
 ARG   0.007   0.000   ARG E 138 

*********************** 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
  105 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
REVERT: E   69 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.5904 (ptpt)
REVERT: E   83 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7834 (mm-40)
REVERT: E  112 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7354 (ttp-170)
REVERT: E  125 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7940 (mm-30)
REVERT: E  158 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8421 (mm)
REVERT: E  198 GLN cc_start: 0.6914 (mt0) cc_final: 0.6256 (tp40)
REVERT: E  219 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.5665 (pmtt)
REVERT: E  348 GLN cc_start: 0.7659 (pt0) cc_final: 0.7218 (pt0)
REVERT: C  109 GLU cc_start: 0.7949 (tp30) cc_final: 0.7379 (mm-30)
REVERT: C  114 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7834 (t80)
REVERT: C  124 GLN cc_start: 0.8699 (mt0) cc_final: 0.7803 (tm-30)
REVERT: C  202 GLU cc_start: 0.4463 (OUTLIER) cc_final: 0.3939 (tp30)
REVERT: C  216 ILE cc_start: 0.5823 (OUTLIER) cc_final: 0.5235 (tp)
REVERT: C  233 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7262 (mtt-85)
REVERT: C  252 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8005 (mt-10)
REVERT: C  300 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7976 (mmm)
REVERT: C  330 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7351 (tt0)
  outliers start: 20
  outliers final: 7
  residues processed: 96
  average time/residue: 1.4543
  time to fit residues: 144.3183
Evaluate side-chains
  100 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   69 LYS
Chi-restraints excluded: chain E residue  158 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  174 LYS
Chi-restraints excluded: chain E residue  219 LYS
Chi-restraints excluded: chain E residue  260 VAL
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue  114 PHE
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  216 ILE
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 ARG
Chi-restraints excluded: chain C residue  300 MET
Chi-restraints excluded: chain C residue  330 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 12 optimal weight:    8.9990
   chunk 29 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    1.9788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.147863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.118635 restraints weight = 4916.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 1.83
r_work: 0.3054 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4713  Z= 0.196
  Angle     :  0.517   5.917   6405  Z= 0.260
  Chirality :  0.039   0.122    733
  Planarity :  0.004   0.034    840
  Dihedral  :  6.190  52.320    641
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 17.85 %
    Favored  : 78.90 %
  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:  0.95 (0.34), residues: 574
  helix:  1.38 (0.37), residues: 218
  sheet:  1.61 (0.57), residues: 78
  loop : -0.21 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP E  81 
 HIS   0.003   0.001   HIS C 101 
 PHE   0.020   0.002   PHE C 314 
 TYR   0.011   0.002   TYR E 278 
 ARG   0.008   0.000   ARG E 138 

********************** 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
  101 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
REVERT: E   69 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.5829 (ptpt)
REVERT: E   83 GLN cc_start: 0.8035 (tp-100) cc_final: 0.7783 (mm-40)
REVERT: E  112 ARG cc_start: 0.7967 (ttm-80) cc_final: 0.7351 (ttp-170)
REVERT: E  124 GLN cc_start: 0.8420 (mt0) cc_final: 0.8132 (mt0)
REVERT: E  125 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7921 (mm-30)
REVERT: E  158 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8378 (mm)
REVERT: E  219 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.5639 (pmtt)
REVERT: E  348 GLN cc_start: 0.7609 (pt0) cc_final: 0.7170 (pt0)
REVERT: C   83 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7670 (pm20)
REVERT: C  109 GLU cc_start: 0.7926 (tp30) cc_final: 0.7360 (mm-30)
REVERT: C  114 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7906 (t80)
REVERT: C  124 GLN cc_start: 0.8710 (mt0) cc_final: 0.7795 (tm-30)
REVERT: C  202 GLU cc_start: 0.4397 (OUTLIER) cc_final: 0.3885 (tp30)
REVERT: C  216 ILE cc_start: 0.5781 (OUTLIER) cc_final: 0.5200 (tp)
REVERT: C  233 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7236 (mtt-85)
REVERT: C  252 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8000 (mt-10)
REVERT: C  300 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7962 (mmm)
REVERT: C  328 SER cc_start: 0.7959 (m) cc_final: 0.7655 (t)
REVERT: C  330 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7343 (tt0)
  outliers start: 16
  outliers final: 6
  residues processed: 93
  average time/residue: 1.3902
  time to fit residues: 133.5435
Evaluate side-chains
  101 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   69 LYS
Chi-restraints excluded: chain E residue  158 LEU
Chi-restraints excluded: chain E residue  167 LEU
Chi-restraints excluded: chain E residue  174 LYS
Chi-restraints excluded: chain E residue  219 LYS
Chi-restraints excluded: chain E residue  260 VAL
Chi-restraints excluded: chain C residue   49 THR
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue  114 PHE
Chi-restraints excluded: chain C residue  173 VAL
Chi-restraints excluded: chain C residue  202 GLU
Chi-restraints excluded: chain C residue  216 ILE
Chi-restraints excluded: chain C residue  231 VAL
Chi-restraints excluded: chain C residue  233 ARG
Chi-restraints excluded: chain C residue  300 MET
Chi-restraints excluded: chain C residue  330 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 25 optimal weight:    0.0870
   chunk 27 optimal weight:    5.9990
   chunk 30 optimal weight:    9.9990
   chunk 6 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 2 optimal weight:    8.9990
   chunk 31 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9990
   chunk 43 optimal weight:    8.9990
   chunk 8 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   overall best weight:    1.1962

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

Flipped N/Q/H residues before XYZ refinement:
C 239 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.149570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.120597 restraints weight = 4901.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 1.83
r_work: 0.3080 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4713  Z= 0.149
  Angle     :  0.486   5.641   6405  Z= 0.244
  Chirality :  0.038   0.124    733
  Planarity :  0.004   0.033    840
  Dihedral  :  6.008  53.419    641
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 18.26 %
    Favored  : 78.30 %
  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:  1.08 (0.35), residues: 574
  helix:  1.49 (0.37), residues: 219
  sheet:  1.44 (0.56), residues: 83
  loop : -0.09 (0.35), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP E  81 
 HIS   0.003   0.001   HIS C 101 
 PHE   0.018   0.002   PHE C 314 
 TYR   0.014   0.001   TYR E 278 
 ARG   0.007   0.000   ARG E 138 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4740.14 seconds
wall clock time: 84 minutes 9.76 seconds (5049.76 seconds total)