Starting phenix.real_space_refine
on Sun Apr 27 04:43:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nt5_0502/04_2025/6nt5_0502_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nt5_0502/04_2025/6nt5_0502.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nt5_0502/04_2025/6nt5_0502.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nt5_0502/04_2025/6nt5_0502.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nt5_0502/04_2025/6nt5_0502_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nt5_0502/04_2025/6nt5_0502_neut.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      24      5.16       5
     C    2952      2.51       5
     N     798      2.21       5
     O     812      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 4586
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2293
          Classifications: {'peptide': 292}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 13, 'TRANS': 278}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 18
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.67, per 1000 atoms: 0.80
  Number of scatterers: 4586
  At special positions: 0
  Unit cell: (78.12, 73.08, 104.16, 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      24     16.00
     O     812      8.00
     N     798      7.00
     C    2952      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: 1.06
  Conformation dependent library (CDL) restraints added in 535.1 milliseconds
  

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1100

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 2 sheets defined
      60.6% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 33
      removed outlier: 3.846A  pdb=" N   LEU A  30 " --> pdb=" O   LEU A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 70
      removed outlier: 3.763A  pdb=" N   GLU A  68 " --> pdb=" O   CYS A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 89
    Processing helix  chain 'A' and resid 91 through 105
      removed outlier: 3.612A  pdb=" N   ARG A  95 " --> pdb=" O   CYS A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 134
      removed outlier: 3.765A  pdb=" N   LEU A 123 " --> pdb=" O   TRP A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 149
    Processing helix  chain 'A' and resid 156 through 167
      removed outlier: 3.684A  pdb=" N   ALA A 160 " --> pdb=" O   ALA A 156 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   TYR A 167 " --> pdb=" O   TYR A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 172
    Processing helix  chain 'A' and resid 174 through 183
    Processing helix  chain 'A' and resid 183 through 188
      removed outlier: 4.134A  pdb=" N   ASN A 188 " --> pdb=" O   GLN A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 273
      removed outlier: 4.179A  pdb=" N   THR A 267 " --> pdb=" O   THR A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 278
      removed outlier: 3.528A  pdb=" N   ALA A 277 " --> pdb=" O   TYR A 274 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLY A 278 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 274 through 278'
    Processing helix  chain 'A' and resid 280 through 301
      removed outlier: 3.746A  pdb=" N   ASP A 301 " --> pdb=" O   ASP A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 336
      removed outlier: 3.699A  pdb=" N   GLU A 328 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 33
      removed outlier: 3.846A  pdb=" N   LEU B  30 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 70
      removed outlier: 3.762A  pdb=" N   GLU B  68 " --> pdb=" O   CYS B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 89
    Processing helix  chain 'B' and resid 91 through 105
      removed outlier: 3.612A  pdb=" N   ARG B  95 " --> pdb=" O   CYS B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 134
      removed outlier: 3.766A  pdb=" N   LEU B 123 " --> pdb=" O   TRP B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 149
    Processing helix  chain 'B' and resid 156 through 167
      removed outlier: 3.683A  pdb=" N   ALA B 160 " --> pdb=" O   ALA B 156 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   TYR B 167 " --> pdb=" O   TYR B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 172
    Processing helix  chain 'B' and resid 174 through 183
    Processing helix  chain 'B' and resid 183 through 188
      removed outlier: 4.134A  pdb=" N   ASN B 188 " --> pdb=" O   GLN B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 273
      removed outlier: 4.179A  pdb=" N   THR B 267 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 278
      removed outlier: 3.529A  pdb=" N   ALA B 277 " --> pdb=" O   TYR B 274 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLY B 278 " --> pdb=" O   SER B 275 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 274 through 278'
    Processing helix  chain 'B' and resid 280 through 301
      removed outlier: 3.748A  pdb=" N   ASP B 301 " --> pdb=" O   ASP B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 336
      removed outlier: 3.699A  pdb=" N   GLU B 328 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 223
      removed outlier: 5.944A  pdb=" N   PHE A 221 " --> pdb=" O   GLU A 246 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   GLU A 246 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   GLY A 255 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   LEU A 198 " --> pdb=" O   ARG A 310 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   ILE A 312 " --> pdb=" O   LEU A 198 " (cutoff:3.500A)
      removed outlier: 5.787A  pdb=" N   ILE A 200 " --> pdb=" O   ILE A 312 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   TYR A 314 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   LEU A 202 " --> pdb=" O   TYR A 314 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 219 through 223
      removed outlier: 5.945A  pdb=" N   PHE B 221 " --> pdb=" O   GLU B 246 " (cutoff:3.500A)
      removed outlier: 5.842A  pdb=" N   GLU B 246 " --> pdb=" O   PHE B 221 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   GLY B 255 " --> pdb=" O   LEU B 247 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   LEU B 198 " --> pdb=" O   ARG B 310 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   ILE B 312 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 5.786A  pdb=" N   ILE B 200 " --> pdb=" O   ILE B 312 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   TYR B 314 " --> pdb=" O   ILE B 200 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   LEU B 202 " --> pdb=" O   TYR B 314 " (cutoff:3.500A)

    236 hydrogen bonds defined for protein.
    702 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: 1.03

  Time building geometry restraints manager: 1.28 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: 1437
        1.34 -     1.45: 710
        1.45 -     1.57: 2501
        1.57 -     1.69: 0
        1.69 -     1.81: 28
  Bond restraints: 4676
  Sorted by residual:
  bond pdb=" CA  GLY B  90 "
       pdb=" C   GLY B  90 "
    ideal  model  delta    sigma   weight residual
    1.530  1.511  0.020 1.04e-02 9.25e+03 3.67e+00
  bond pdb=" CA  GLY A  90 "
       pdb=" C   GLY A  90 "
    ideal  model  delta    sigma   weight residual
    1.530  1.511  0.019 1.04e-02 9.25e+03 3.50e+00
  bond pdb=" N   GLY B  90 "
       pdb=" CA  GLY B  90 "
    ideal  model  delta    sigma   weight residual
    1.464  1.447  0.018 1.12e-02 7.97e+03 2.44e+00
  bond pdb=" N   GLY A  90 "
       pdb=" CA  GLY A  90 "
    ideal  model  delta    sigma   weight residual
    1.464  1.447  0.017 1.12e-02 7.97e+03 2.36e+00
  bond pdb=" C   PRO A  11 "
       pdb=" N   CYS A  12 "
    ideal  model  delta    sigma   weight residual
    1.329  1.300  0.029 1.86e-02 2.89e+03 2.35e+00
  ... (remaining 4671 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 6141
        2.26 -     4.52: 171
        4.52 -     6.79: 18
        6.79 -     9.05: 10
        9.05 -    11.31: 2
  Bond angle restraints: 6342
  Sorted by residual:
  angle pdb=" N   LEU B 172 "
        pdb=" CA  LEU B 172 "
        pdb=" C   LEU B 172 "
      ideal   model   delta    sigma   weight residual
     109.81  121.12  -11.31 2.21e+00 2.05e-01 2.62e+01
  angle pdb=" N   LEU A 172 "
        pdb=" CA  LEU A 172 "
        pdb=" C   LEU A 172 "
      ideal   model   delta    sigma   weight residual
     109.81  121.11  -11.30 2.21e+00 2.05e-01 2.62e+01
  angle pdb=" C   GLY B 151 "
        pdb=" N   ASN B 152 "
        pdb=" CA  ASN B 152 "
      ideal   model   delta    sigma   weight residual
     122.08  128.79   -6.71 1.47e+00 4.63e-01 2.09e+01
  angle pdb=" C   GLY A 151 "
        pdb=" N   ASN A 152 "
        pdb=" CA  ASN A 152 "
      ideal   model   delta    sigma   weight residual
     122.08  128.75   -6.67 1.47e+00 4.63e-01 2.06e+01
  angle pdb=" C   PRO A  11 "
        pdb=" N   CYS A  12 "
        pdb=" CA  CYS A  12 "
      ideal   model   delta    sigma   weight residual
     121.48  129.66   -8.18 2.04e+00 2.40e-01 1.61e+01
  ... (remaining 6337 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.52: 2634
       14.52 -    29.04: 108
       29.04 -    43.56: 34
       43.56 -    58.08: 3
       58.08 -    72.60: 7
  Dihedral angle restraints: 2786
    sinusoidal: 1086
      harmonic: 1700
  Sorted by residual:
  dihedral pdb=" CA  ASP B 223 "
           pdb=" C   ASP B 223 "
           pdb=" N   LYS B 224 "
           pdb=" CA  LYS B 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.02   17.98     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  ASP A 223 "
           pdb=" C   ASP A 223 "
           pdb=" N   LYS A 224 "
           pdb=" CA  LYS A 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.04   17.96     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  TYR A 245 "
           pdb=" C   TYR A 245 "
           pdb=" N   GLU A 246 "
           pdb=" CA  GLU A 246 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.45   17.55     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 2783 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 559
       0.055 -    0.109: 141
       0.109 -    0.164: 24
       0.164 -    0.218: 2
       0.218 -    0.273: 4
  Chirality restraints: 730
  Sorted by residual:
  chirality pdb=" CA  LEU A 172 "
            pdb=" N   LEU A 172 "
            pdb=" C   LEU A 172 "
            pdb=" CB  LEU A 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CA  LEU B 172 "
            pdb=" N   LEU B 172 "
            pdb=" C   LEU B 172 "
            pdb=" CB  LEU B 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CA  ASN A 152 "
            pdb=" N   ASN A 152 "
            pdb=" C   ASN A 152 "
            pdb=" CB  ASN A 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.42e+00
  ... (remaining 727 not shown)

  Planarity restraints: 798
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 172 "   -0.036 5.00e-02 4.00e+02   5.37e-02 4.61e+00
        pdb=" N   PRO A 173 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 173 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 173 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 172 "   -0.036 5.00e-02 4.00e+02   5.34e-02 4.57e+00
        pdb=" N   PRO B 173 "    0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 173 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 173 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A   7 "    0.032 5.00e-02 4.00e+02   4.81e-02 3.70e+00
        pdb=" N   PRO A   8 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A   8 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A   8 "    0.027 5.00e-02 4.00e+02
  ... (remaining 795 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1337
        2.82 -     3.34: 4039
        3.34 -     3.86: 7068
        3.86 -     4.38: 7543
        4.38 -     4.90: 13049
  Nonbonded interactions: 33036
  Sorted by model distance:
  nonbonded pdb=" O   TYR A  81 "
            pdb=" OG1 THR A  84 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   TYR B  81 "
            pdb=" OG1 THR B  84 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   LEU A 124 "
            pdb=" OG  SER A 127 "
     model   vdw
     2.388 3.040
  nonbonded pdb=" O   LEU B 124 "
            pdb=" OG  SER B 127 "
     model   vdw
     2.390 3.040
  nonbonded pdb=" O   HIS A  50 "
            pdb=" OG  SER A  53 "
     model   vdw
     2.461 3.040
  ... (remaining 33031 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 group one per residue
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:             0.720
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.990
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   4676  Z= 0.296
  Angle     :  0.931  11.310   6342  Z= 0.495
  Chirality :  0.053   0.273    730
  Planarity :  0.008   0.054    798
  Dihedral  : 10.321  72.601   1686
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  1.23 %
    Favored  : 98.35 %
  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: -2.40 (0.29), residues: 552
  helix: -1.14 (0.24), residues: 304
  sheet: -1.41 (0.79), residues: 28
  loop : -2.13 (0.35), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B  82 
 HIS   0.007   0.002   HIS B 157 
 PHE   0.019   0.003   PHE A 153 
 TYR   0.032   0.003   TYR B 199 
 ARG   0.011   0.001   ARG A 178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10373 (  236)
  hydrogen bonds       : angle       5.57110 (  702)
  covalent geometry    : bond        0.00638 ( 4676)
  covalent geometry    : angle       0.93095 ( 6342)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 127
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASN cc_start: 0.8973 (t0) cc_final: 0.8579 (t0)
REVERT: A   93 LEU cc_start: 0.8599 (mt) cc_final: 0.8245 (pp)
REVERT: A  119 TRP cc_start: 0.7263 (p90) cc_final: 0.7051 (p90)
REVERT: A  183 ASN cc_start: 0.7717 (m-40) cc_final: 0.6849 (p0)
REVERT: A  223 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.7884 (m-30)
REVERT: B   61 ASN cc_start: 0.8981 (t0) cc_final: 0.8585 (t0)
REVERT: B   93 LEU cc_start: 0.8635 (mt) cc_final: 0.8278 (pp)
REVERT: B  104 TYR cc_start: 0.7430 (t80) cc_final: 0.7212 (t80)
REVERT: B  154 ASN cc_start: 0.8612 (t0) cc_final: 0.8310 (p0)
REVERT: B  183 ASN cc_start: 0.7659 (m-40) cc_final: 0.6804 (p0)
REVERT: B  223 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.7878 (m-30)
  outliers start: 2
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1520
  time to fit residues: 25.3550
Evaluate side-chains
  51 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 15 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 23 optimal weight:    0.1980
   chunk 45 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 196 GLN
A 287 GLN
B 196 GLN
B 287 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.081578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.068435 restraints weight = 18900.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.070276 restraints weight = 10308.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.071503 restraints weight = 6753.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4676  Z= 0.099
  Angle     :  0.545   6.662   6342  Z= 0.269
  Chirality :  0.040   0.139    730
  Planarity :  0.005   0.033    798
  Dihedral  :  4.597  17.433    638
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  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: -0.01 (0.35), residues: 552
  helix:  0.96 (0.28), residues: 318
  sheet: -0.02 (0.85), residues: 28
  loop : -1.54 (0.40), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A  82 
 HIS   0.007   0.001   HIS B  50 
 PHE   0.006   0.001   PHE A 279 
 TYR   0.013   0.001   TYR A 199 
 ARG   0.002   0.000   ARG A 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03027 (  236)
  hydrogen bonds       : angle       3.80151 (  702)
  covalent geometry    : bond        0.00210 ( 4676)
  covalent geometry    : angle       0.54506 ( 6342)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 LEU cc_start: 0.8583 (mt) cc_final: 0.8235 (pp)
REVERT: A  100 LEU cc_start: 0.9111 (mm) cc_final: 0.8901 (tt)
REVERT: A  183 ASN cc_start: 0.7729 (m-40) cc_final: 0.6948 (p0)
REVERT: B  154 ASN cc_start: 0.8571 (t0) cc_final: 0.8335 (p0)
REVERT: B  155 VAL cc_start: 0.9094 (t) cc_final: 0.8693 (p)
REVERT: B  183 ASN cc_start: 0.7517 (m-40) cc_final: 0.6767 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1174
  time to fit residues: 15.1103
Evaluate side-chains
  50 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 21 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 54 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0070
   chunk 35 optimal weight:    8.9990
   chunk 3 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:    9.9990
   chunk 44 optimal weight:    9.9990
   overall best weight:    2.1204

-------------------------------------------------------------------------------
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 = 0.3432 r_free = 0.3432 target = 0.079491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.066395 restraints weight = 19137.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.068145 restraints weight = 10356.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.069364 restraints weight = 6829.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4676  Z= 0.130
  Angle     :  0.550   6.644   6342  Z= 0.272
  Chirality :  0.041   0.186    730
  Planarity :  0.004   0.028    798
  Dihedral  :  4.256  15.438    638
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  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:  0.94 (0.36), residues: 552
  helix:  1.76 (0.30), residues: 318
  sheet:  0.00 (0.86), residues: 28
  loop : -1.12 (0.42), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 161 
 HIS   0.002   0.001   HIS A  16 
 PHE   0.007   0.001   PHE B 269 
 TYR   0.014   0.001   TYR A 199 
 ARG   0.002   0.000   ARG A 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03158 (  236)
  hydrogen bonds       : angle       3.64161 (  702)
  covalent geometry    : bond        0.00295 ( 4676)
  covalent geometry    : angle       0.54963 ( 6342)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  155 VAL cc_start: 0.9062 (t) cc_final: 0.8674 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.1950
  time to fit residues: 15.7565
Evaluate side-chains
  32 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 36 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 2 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   chunk 46 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0670
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.7724

-------------------------------------------------------------------------------
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 = 0.3431 r_free = 0.3431 target = 0.079792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.066972 restraints weight = 19018.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.068720 restraints weight = 10452.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.069936 restraints weight = 6899.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.3287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4676  Z= 0.113
  Angle     :  0.518   5.928   6342  Z= 0.252
  Chirality :  0.039   0.130    730
  Planarity :  0.003   0.025    798
  Dihedral  :  4.090  15.357    638
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  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:  1.30 (0.37), residues: 552
  helix:  2.03 (0.30), residues: 318
  sheet: -0.10 (0.91), residues: 28
  loop : -0.89 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 119 
 HIS   0.002   0.001   HIS B  50 
 PHE   0.009   0.001   PHE B 117 
 TYR   0.012   0.001   TYR A 199 
 ARG   0.002   0.000   ARG B 178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02902 (  236)
  hydrogen bonds       : angle       3.49364 (  702)
  covalent geometry    : bond        0.00259 ( 4676)
  covalent geometry    : angle       0.51752 ( 6342)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  155 VAL cc_start: 0.9052 (t) cc_final: 0.8644 (p)
REVERT: B  208 VAL cc_start: 0.9200 (t) cc_final: 0.8910 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.1438
  time to fit residues: 10.9073
Evaluate side-chains
  35 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 42 optimal weight:    4.9990
   chunk 39 optimal weight:    6.9990
   chunk 23 optimal weight:    8.9990
   chunk 9 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 3 optimal weight:   10.0000
   chunk 55 optimal weight:    8.9990
   chunk 17 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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 = 0.3359 r_free = 0.3359 target = 0.076426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.063347 restraints weight = 19717.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.064993 restraints weight = 10750.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.066144 restraints weight = 7189.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.3623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   4676  Z= 0.243
  Angle     :  0.688   7.680   6342  Z= 0.331
  Chirality :  0.043   0.146    730
  Planarity :  0.004   0.026    798
  Dihedral  :  4.538  15.417    638
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  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 (0.37), residues: 552
  helix:  1.60 (0.30), residues: 320
  sheet: -0.32 (0.96), residues: 28
  loop : -0.77 (0.45), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 119 
 HIS   0.004   0.001   HIS A  50 
 PHE   0.015   0.002   PHE A 269 
 TYR   0.019   0.002   TYR B 199 
 ARG   0.004   0.001   ARG A 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04197 (  236)
  hydrogen bonds       : angle       4.10837 (  702)
  covalent geometry    : bond        0.00548 ( 4676)
  covalent geometry    : angle       0.68837 ( 6342)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.566 
Fit side-chains
REVERT: A  155 VAL cc_start: 0.9207 (t) cc_final: 0.8860 (p)
REVERT: B  155 VAL cc_start: 0.9190 (t) cc_final: 0.8847 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1208
  time to fit residues: 8.7689
Evaluate side-chains
  28 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 22 optimal weight:    0.4980
   chunk 42 optimal weight:    5.9990
   chunk 35 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 17 optimal weight:    0.0570
   chunk 25 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 52 optimal weight:    0.2980
   overall best weight:    0.5298

-------------------------------------------------------------------------------
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 = 0.3431 r_free = 0.3431 target = 0.079951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.066993 restraints weight = 18935.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.068768 restraints weight = 10283.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.070033 restraints weight = 6754.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.3846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   4676  Z= 0.092
  Angle     :  0.507   5.858   6342  Z= 0.249
  Chirality :  0.039   0.174    730
  Planarity :  0.003   0.027    798
  Dihedral  :  3.987  16.309    638
  Min Nonbonded Distance : 2.655

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  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:  1.48 (0.37), residues: 552
  helix:  2.09 (0.30), residues: 318
  sheet: -0.28 (0.92), residues: 28
  loop : -0.59 (0.45), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 119 
 HIS   0.003   0.001   HIS B 157 
 PHE   0.008   0.001   PHE B 117 
 TYR   0.009   0.001   TYR A 199 
 ARG   0.002   0.000   ARG B  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02778 (  236)
  hydrogen bonds       : angle       3.42934 (  702)
  covalent geometry    : bond        0.00193 ( 4676)
  covalent geometry    : angle       0.50664 ( 6342)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.484 
Fit side-chains
REVERT: A  100 LEU cc_start: 0.9165 (mm) cc_final: 0.8916 (tt)
REVERT: A  155 VAL cc_start: 0.9066 (t) cc_final: 0.8723 (p)
REVERT: A  223 ASP cc_start: 0.8014 (t0) cc_final: 0.7507 (t70)
REVERT: B  155 VAL cc_start: 0.9041 (t) cc_final: 0.8664 (p)
REVERT: B  223 ASP cc_start: 0.8042 (t0) cc_final: 0.7513 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.1241
  time to fit residues: 10.6352
Evaluate side-chains
  32 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 22 optimal weight:    0.8980
   chunk 31 optimal weight:   10.0000
   chunk 15 optimal weight:    0.1980
   chunk 37 optimal weight:    9.9990
   chunk 4 optimal weight:    0.8980
   chunk 20 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 52 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.080443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.067540 restraints weight = 18842.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.069401 restraints weight = 10394.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.070606 restraints weight = 6783.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.4051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4676  Z= 0.090
  Angle     :  0.500   6.702   6342  Z= 0.240
  Chirality :  0.038   0.138    730
  Planarity :  0.003   0.026    798
  Dihedral  :  3.811  16.012    638
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  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:  1.78 (0.38), residues: 552
  helix:  2.29 (0.30), residues: 322
  sheet:  0.05 (0.90), residues: 28
  loop : -0.48 (0.46), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 161 
 HIS   0.003   0.000   HIS B 157 
 PHE   0.005   0.001   PHE B 153 
 TYR   0.011   0.001   TYR B 199 
 ARG   0.002   0.000   ARG A  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02669 (  236)
  hydrogen bonds       : angle       3.38332 (  702)
  covalent geometry    : bond        0.00200 ( 4676)
  covalent geometry    : angle       0.50018 ( 6342)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.544 
Fit side-chains
REVERT: A  100 LEU cc_start: 0.9136 (mm) cc_final: 0.8893 (tt)
REVERT: A  155 VAL cc_start: 0.9026 (t) cc_final: 0.8635 (p)
REVERT: A  223 ASP cc_start: 0.8065 (t0) cc_final: 0.7430 (t70)
REVERT: B  155 VAL cc_start: 0.8828 (t) cc_final: 0.8403 (p)
REVERT: B  223 ASP cc_start: 0.8081 (t0) cc_final: 0.7450 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.1178
  time to fit residues: 10.0342
Evaluate side-chains
  33 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 16 optimal weight:    0.4980
   chunk 25 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 55 optimal weight:    8.9990
   chunk 35 optimal weight:    8.9990
   chunk 34 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 48 optimal weight:    7.9990
   overall best weight:    3.0586

-------------------------------------------------------------------------------
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 = 0.3399 r_free = 0.3399 target = 0.078290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.065396 restraints weight = 18881.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.067127 restraints weight = 10279.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.068308 restraints weight = 6793.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.4025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4676  Z= 0.162
  Angle     :  0.579   6.400   6342  Z= 0.278
  Chirality :  0.041   0.142    730
  Planarity :  0.003   0.026    798
  Dihedral  :  4.055  15.643    638
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  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:  1.42 (0.38), residues: 552
  helix:  2.12 (0.30), residues: 320
  sheet: -0.61 (0.76), residues: 46
  loop : -0.72 (0.48), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 119 
 HIS   0.005   0.001   HIS A 157 
 PHE   0.010   0.001   PHE B 269 
 TYR   0.015   0.001   TYR B 199 
 ARG   0.002   0.000   ARG A 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03280 (  236)
  hydrogen bonds       : angle       3.70539 (  702)
  covalent geometry    : bond        0.00370 ( 4676)
  covalent geometry    : angle       0.57944 ( 6342)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.552 
Fit side-chains
REVERT: B  155 VAL cc_start: 0.9101 (t) cc_final: 0.8719 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.1249
  time to fit residues: 8.6341
Evaluate side-chains
  26 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 56 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 45 optimal weight:    0.5980
   chunk 57 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 11 optimal weight:   10.0000
   chunk 19 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   overall best weight:    2.0384

-------------------------------------------------------------------------------
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 = 0.3406 r_free = 0.3406 target = 0.078617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.065434 restraints weight = 18949.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.067155 restraints weight = 10371.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.068359 restraints weight = 6923.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.4193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4676  Z= 0.123
  Angle     :  0.550   6.699   6342  Z= 0.271
  Chirality :  0.040   0.140    730
  Planarity :  0.003   0.026    798
  Dihedral  :  4.005  15.758    638
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  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:  1.33 (0.38), residues: 552
  helix:  2.01 (0.30), residues: 322
  sheet: -0.51 (0.76), residues: 46
  loop : -0.77 (0.47), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 119 
 HIS   0.008   0.001   HIS A  50 
 PHE   0.006   0.001   PHE B 269 
 TYR   0.012   0.001   TYR B 199 
 ARG   0.002   0.000   ARG B 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03171 (  236)
  hydrogen bonds       : angle       3.57552 (  702)
  covalent geometry    : bond        0.00282 ( 4676)
  covalent geometry    : angle       0.54999 ( 6342)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 TRP cc_start: 0.7575 (p90) cc_final: 0.6879 (p90)
REVERT: B  119 TRP cc_start: 0.7510 (p90) cc_final: 0.6733 (p90)
REVERT: B  155 VAL cc_start: 0.8980 (t) cc_final: 0.8613 (p)
REVERT: B  296 GLU cc_start: 0.8019 (pt0) cc_final: 0.7671 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 47
  average time/residue: 0.1279
  time to fit residues: 8.9031
Evaluate side-chains
  28 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 39 optimal weight:    9.9990
   chunk 54 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 29 optimal weight:    0.6980
   chunk 31 optimal weight:    8.9990
   chunk 26 optimal weight:    6.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
A  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.078180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.065425 restraints weight = 18672.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.067172 restraints weight = 10260.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.068359 restraints weight = 6716.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.4207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4676  Z= 0.145
  Angle     :  0.582   6.443   6342  Z= 0.287
  Chirality :  0.040   0.142    730
  Planarity :  0.003   0.026    798
  Dihedral  :  4.075  15.507    638
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.23 (0.38), residues: 552
  helix:  1.91 (0.30), residues: 324
  sheet: -0.52 (0.76), residues: 46
  loop : -0.80 (0.47), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 119 
 HIS   0.011   0.001   HIS B  50 
 PHE   0.008   0.001   PHE B 269 
 TYR   0.014   0.001   TYR B 199 
 ARG   0.002   0.000   ARG B  45 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03372 (  236)
  hydrogen bonds       : angle       3.69983 (  702)
  covalent geometry    : bond        0.00332 ( 4676)
  covalent geometry    : angle       0.58247 ( 6342)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 TRP cc_start: 0.7579 (p90) cc_final: 0.6811 (p90)
REVERT: B  119 TRP cc_start: 0.7553 (p90) cc_final: 0.6743 (p90)
REVERT: B  155 VAL cc_start: 0.9057 (t) cc_final: 0.8709 (p)
REVERT: B  296 GLU cc_start: 0.8142 (pt0) cc_final: 0.7697 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.1422
  time to fit residues: 9.0485
Evaluate side-chains
  31 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 30 optimal weight:    9.9990
   chunk 26 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3410 r_free = 0.3410 target = 0.079134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.066120 restraints weight = 18664.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.067862 restraints weight = 10218.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.069022 restraints weight = 6763.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.4333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4676  Z= 0.105
  Angle     :  0.533   6.454   6342  Z= 0.262
  Chirality :  0.039   0.139    730
  Planarity :  0.003   0.042    798
  Dihedral  :  3.936  15.545    638
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.45 (0.38), residues: 552
  helix:  2.10 (0.30), residues: 322
  sheet: -0.42 (0.76), residues: 46
  loop : -0.72 (0.47), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 119 
 HIS   0.003   0.001   HIS B  50 
 PHE   0.004   0.001   PHE B 279 
 TYR   0.011   0.001   TYR B 199 
 ARG   0.002   0.000   ARG B 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02969 (  236)
  hydrogen bonds       : angle       3.51484 (  702)
  covalent geometry    : bond        0.00238 ( 4676)
  covalent geometry    : angle       0.53320 ( 6342)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1589.22 seconds
wall clock time: 28 minutes 46.95 seconds (1726.95 seconds total)