Starting phenix.real_space_refine
on Tue Feb 11 06:53:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nt5_0502/02_2025/6nt5_0502_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nt5_0502/02_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_0502/02_2025/6nt5_0502.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nt5_0502/02_2025/6nt5_0502.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nt5_0502/02_2025/6nt5_0502_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nt5_0502/02_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-5592/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: 3.07, per 1000 atoms: 0.67
  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: 1.09
  Conformation dependent library (CDL) restraints added in 463.3 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: 0.49
  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: 1.18

  Time building geometry restraints manager: 1.26 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:             0.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.410
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.980
-------------------------------------------------------------------------------
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= 0.420
  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 

*********************** 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  : 0.593 
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: 0.1501
  time to fit residues: 25.0989
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  : 0.539 
-------------------------------------------------------------------------------
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 = 41)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.068437 restraints weight = 18900.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.070279 restraints weight = 10303.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.071512 restraints weight = 6749.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
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= 0.135
  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 

*********************** 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  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 LEU cc_start: 0.8584 (mt) cc_final: 0.8235 (pp)
REVERT: A  100 LEU cc_start: 0.9112 (mm) cc_final: 0.8901 (tt)
REVERT: A  183 ASN cc_start: 0.7731 (m-40) cc_final: 0.6948 (p0)
REVERT: B  154 ASN cc_start: 0.8576 (t0) cc_final: 0.8336 (p0)
REVERT: B  155 VAL cc_start: 0.9093 (t) cc_final: 0.8693 (p)
REVERT: B  183 ASN cc_start: 0.7517 (m-40) cc_final: 0.6766 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1150
  time to fit residues: 14.8987
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  : 0.561 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 34 optimal weight:    7.9990
   chunk 6 optimal weight:   10.0000
   chunk 54 optimal weight:    0.6980
   chunk 10 optimal weight:    7.9990
   chunk 35 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   chunk 44 optimal weight:    9.9990
   overall best weight:    4.7388

-------------------------------------------------------------------------------
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 = 0.3368 r_free = 0.3368 target = 0.076589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.063589 restraints weight = 19296.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.065251 restraints weight = 10607.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.066378 restraints weight = 7050.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.3125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   4676  Z= 0.354
  Angle     :  0.699   6.810   6342  Z= 0.344
  Chirality :  0.045   0.200    730
  Planarity :  0.004   0.029    798
  Dihedral  :  4.689  15.221    638
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  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:  0.60 (0.36), residues: 552
  helix:  1.45 (0.29), residues: 318
  sheet: -0.63 (0.87), residues: 28
  loop : -1.11 (0.42), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 119 
 HIS   0.004   0.001   HIS A  16 
 PHE   0.013   0.002   PHE B 269 
 TYR   0.020   0.002   TYR B 199 
 ARG   0.004   0.000   ARG A 197 

*********************** 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
  49 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  155 VAL cc_start: 0.9141 (t) cc_final: 0.8768 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.1238
  time to fit residues: 8.6387
Evaluate side-chains
  29 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    8.9990
   chunk 24 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 46 optimal weight:    8.9990
   chunk 27 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    2.7588

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.078256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.064893 restraints weight = 19394.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.066419 restraints weight = 10828.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.067616 restraints weight = 7491.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.3374

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= 0.229
  Angle     :  0.561   5.922   6342  Z= 0.278
  Chirality :  0.040   0.130    730
  Planarity :  0.004   0.026    798
  Dihedral  :  4.395  15.650    638
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    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:  0.92 (0.36), residues: 552
  helix:  1.66 (0.30), residues: 318
  sheet: -0.51 (0.95), residues: 28
  loop : -0.89 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 119 
 HIS   0.003   0.001   HIS B 157 
 PHE   0.014   0.002   PHE B 117 
 TYR   0.014   0.001   TYR A 199 
 ARG   0.002   0.000   ARG B 178 

*********************** 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
  54 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  296 GLU cc_start: 0.7944 (pt0) cc_final: 0.7684 (tt0)
REVERT: B  155 VAL cc_start: 0.9054 (t) cc_final: 0.8657 (p)
REVERT: B  296 GLU cc_start: 0.7957 (pt0) cc_final: 0.7707 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1584
  time to fit residues: 11.3483
Evaluate side-chains
  29 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 42 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 9 optimal weight:    7.9990
   chunk 7 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 55 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 34 optimal weight:    8.9990
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
B 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.077453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.064317 restraints weight = 19658.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.066012 restraints weight = 10799.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.067182 restraints weight = 7168.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.3685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4676  Z= 0.239
  Angle     :  0.573   6.482   6342  Z= 0.281
  Chirality :  0.041   0.200    730
  Planarity :  0.003   0.029    798
  Dihedral  :  4.277  15.572    638
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  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:  1.01 (0.37), residues: 552
  helix:  1.84 (0.30), residues: 318
  sheet: -0.76 (0.77), residues: 46
  loop : -1.00 (0.47), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 161 
 HIS   0.003   0.001   HIS B 157 
 PHE   0.010   0.002   PHE B 269 
 TYR   0.015   0.001   TYR A 199 
 ARG   0.002   0.000   ARG B 169 

*********************** 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
  51 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.533 
Fit side-chains
REVERT: A  155 VAL cc_start: 0.9137 (t) cc_final: 0.8764 (p)
REVERT: A  296 GLU cc_start: 0.7898 (pt0) cc_final: 0.7619 (tt0)
REVERT: B  155 VAL cc_start: 0.9092 (t) cc_final: 0.8766 (p)
REVERT: B  296 GLU cc_start: 0.7902 (pt0) cc_final: 0.7628 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1130
  time to fit residues: 8.4105
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  : 0.601 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0020
   chunk 9 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 19 optimal weight:   10.0000
   chunk 52 optimal weight:    8.9990
   overall best weight:    0.5588

-------------------------------------------------------------------------------
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 = 0.3429 r_free = 0.3429 target = 0.079882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.066745 restraints weight = 18818.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.068560 restraints weight = 10232.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.069855 restraints weight = 6676.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.3938

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= 0.115
  Angle     :  0.491   6.057   6342  Z= 0.242
  Chirality :  0.038   0.132    730
  Planarity :  0.003   0.027    798
  Dihedral  :  3.909  15.754    638
  Min Nonbonded Distance : 2.656

Molprobity Statistics.
  All-atom Clashscore : 5.88
  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:  1.55 (0.37), residues: 552
  helix:  2.15 (0.30), residues: 318
  sheet:  0.00 (0.92), residues: 28
  loop : -0.62 (0.45), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 119 
 HIS   0.005   0.001   HIS B  50 
 PHE   0.007   0.001   PHE B 117 
 TYR   0.009   0.001   TYR A 199 
 ARG   0.002   0.000   ARG B 334 

*********************** 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
  65 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.627 
Fit side-chains
REVERT: A  100 LEU cc_start: 0.9148 (mm) cc_final: 0.8907 (tt)
REVERT: A  155 VAL cc_start: 0.9052 (t) cc_final: 0.8690 (p)
REVERT: A  223 ASP cc_start: 0.8079 (t0) cc_final: 0.7517 (t70)
REVERT: A  296 GLU cc_start: 0.7946 (pt0) cc_final: 0.7701 (tt0)
REVERT: B  155 VAL cc_start: 0.9003 (t) cc_final: 0.8704 (p)
REVERT: B  223 ASP cc_start: 0.8075 (t0) cc_final: 0.7504 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1279
  time to fit residues: 11.5739
Evaluate side-chains
  38 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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 = 0.3405 r_free = 0.3405 target = 0.078829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.065842 restraints weight = 19323.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.067586 restraints weight = 10506.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.068831 restraints weight = 6911.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.4066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4676  Z= 0.174
  Angle     :  0.526   6.707   6342  Z= 0.254
  Chirality :  0.039   0.123    730
  Planarity :  0.003   0.027    798
  Dihedral  :  3.929  15.828    638
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  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:  1.49 (0.38), residues: 552
  helix:  2.19 (0.30), residues: 320
  sheet: -0.57 (0.76), residues: 46
  loop : -0.74 (0.48), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 161 
 HIS   0.002   0.000   HIS B 157 
 PHE   0.007   0.001   PHE B 269 
 TYR   0.013   0.001   TYR A 199 
 ARG   0.002   0.000   ARG B  14 

*********************** 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  : 0.562 
Fit side-chains
REVERT: A  100 LEU cc_start: 0.9155 (mm) cc_final: 0.8903 (tt)
REVERT: A  155 VAL cc_start: 0.9153 (t) cc_final: 0.8766 (p)
REVERT: A  223 ASP cc_start: 0.8201 (t0) cc_final: 0.7536 (t70)
REVERT: A  296 GLU cc_start: 0.8007 (pt0) cc_final: 0.7779 (tt0)
REVERT: B  155 VAL cc_start: 0.9098 (t) cc_final: 0.8814 (p)
REVERT: B  223 ASP cc_start: 0.8188 (t0) cc_final: 0.7531 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.1164
  time to fit residues: 9.9130
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  : 0.541 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 16 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    8.9990
   chunk 55 optimal weight:    7.9990
   chunk 35 optimal weight:    0.7980
   chunk 34 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   overall best weight:    4.1588

-------------------------------------------------------------------------------
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 = 0.076557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.062930 restraints weight = 19327.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.064698 restraints weight = 10620.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.065871 restraints weight = 6944.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.4105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   4676  Z= 0.311
  Angle     :  0.660   7.148   6342  Z= 0.321
  Chirality :  0.042   0.153    730
  Planarity :  0.004   0.028    798
  Dihedral  :  4.340  15.243    638
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  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:  0.90 (0.37), residues: 552
  helix:  1.65 (0.30), residues: 322
  sheet: -0.69 (0.76), residues: 46
  loop : -0.93 (0.46), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 119 
 HIS   0.012   0.001   HIS A  50 
 PHE   0.013   0.002   PHE B 269 
 TYR   0.016   0.002   TYR B 199 
 ARG   0.004   0.001   ARG B 169 

*********************** 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
  49 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 VAL cc_start: 0.9312 (t) cc_final: 0.8956 (p)
REVERT: A  296 GLU cc_start: 0.8001 (pt0) cc_final: 0.7724 (tt0)
REVERT: B  155 VAL cc_start: 0.9225 (t) cc_final: 0.8975 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.2083
  time to fit residues: 14.3637
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  : 1.060 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 6 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 19 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.3356 r_free = 0.3356 target = 0.076530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.063036 restraints weight = 19387.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.064736 restraints weight = 10711.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.065896 restraints weight = 7083.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.4300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4676  Z= 0.301
  Angle     :  0.630   6.405   6342  Z= 0.311
  Chirality :  0.042   0.146    730
  Planarity :  0.004   0.027    798
  Dihedral  :  4.425  15.293    638
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  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:  0.80 (0.36), residues: 552
  helix:  1.46 (0.29), residues: 320
  sheet: -0.37 (0.93), residues: 28
  loop : -0.81 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 119 
 HIS   0.007   0.001   HIS A  50 
 PHE   0.011   0.002   PHE A 269 
 TYR   0.016   0.002   TYR A 199 
 ARG   0.004   0.000   ARG B 293 

*********************** 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
  44 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 TRP cc_start: 0.7709 (p90) cc_final: 0.6900 (p90)
REVERT: A  155 VAL cc_start: 0.9263 (t) cc_final: 0.8874 (p)
REVERT: A  296 GLU cc_start: 0.8079 (pt0) cc_final: 0.7787 (tt0)
REVERT: B  119 TRP cc_start: 0.7622 (p90) cc_final: 0.6829 (p90)
REVERT: B  155 VAL cc_start: 0.9177 (t) cc_final: 0.8914 (p)
REVERT: B  296 GLU cc_start: 0.8193 (pt0) cc_final: 0.7791 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.1226
  time to fit residues: 7.8419
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  : 0.498 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 39 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 9 optimal weight:    9.9990
   chunk 29 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   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 = 0.3389 r_free = 0.3389 target = 0.078202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.065109 restraints weight = 18804.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.066805 restraints weight = 10197.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.067948 restraints weight = 6754.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.4400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4676  Z= 0.154
  Angle     :  0.527   6.648   6342  Z= 0.259
  Chirality :  0.039   0.129    730
  Planarity :  0.003   0.027    798
  Dihedral  :  4.067  15.403    638
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  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:  1.24 (0.37), residues: 552
  helix:  1.84 (0.30), residues: 320
  sheet: -0.23 (0.94), residues: 28
  loop : -0.65 (0.45), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A  50 
 PHE   0.004   0.001   PHE B 269 
 TYR   0.012   0.001   TYR A 199 
 ARG   0.001   0.000   ARG A 293 

********************** 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
  57 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 TRP cc_start: 0.7608 (p90) cc_final: 0.6799 (p90)
REVERT: A  155 VAL cc_start: 0.9215 (t) cc_final: 0.8842 (p)
REVERT: A  223 ASP cc_start: 0.8135 (t0) cc_final: 0.7593 (t70)
REVERT: A  296 GLU cc_start: 0.7898 (pt0) cc_final: 0.7640 (tt0)
REVERT: B  119 TRP cc_start: 0.7576 (p90) cc_final: 0.6768 (p90)
REVERT: B  155 VAL cc_start: 0.9108 (t) cc_final: 0.8852 (p)
REVERT: B  223 ASP cc_start: 0.8141 (t0) cc_final: 0.7574 (t70)
REVERT: B  296 GLU cc_start: 0.7995 (pt0) cc_final: 0.7678 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1136
  time to fit residues: 9.2635
Evaluate side-chains
  36 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 4 optimal weight:   10.0000
   chunk 44 optimal weight:    1.9990
   chunk 36 optimal weight:   10.0000
   chunk 10 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 26 optimal weight:    0.1980
   chunk 51 optimal weight:    0.0670
   chunk 0 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    1.0524

-------------------------------------------------------------------------------
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 = 0.3404 r_free = 0.3404 target = 0.079095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.066450 restraints weight = 18708.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.068239 restraints weight = 10114.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.069432 restraints weight = 6544.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.4479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4676  Z= 0.129
  Angle     :  0.513   6.449   6342  Z= 0.251
  Chirality :  0.038   0.128    730
  Planarity :  0.003   0.028    798
  Dihedral  :  3.893  15.427    638
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  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:  1.42 (0.38), residues: 552
  helix:  1.92 (0.30), residues: 322
  sheet: -0.10 (0.91), residues: 28
  loop : -0.48 (0.46), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 119 
 HIS   0.011   0.001   HIS B  50 
 PHE   0.008   0.001   PHE B 117 
 TYR   0.011   0.001   TYR A 199 
 ARG   0.003   0.000   ARG B  45 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1425.16 seconds
wall clock time: 26 minutes 13.89 seconds (1573.89 seconds total)