Starting phenix.real_space_refine
on Wed Mar  5 22:52:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rsq_24677/03_2025/7rsq_24677.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rsq_24677/03_2025/7rsq_24677.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rsq_24677/03_2025/7rsq_24677.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rsq_24677/03_2025/7rsq_24677.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rsq_24677/03_2025/7rsq_24677.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rsq_24677/03_2025/7rsq_24677.cif"
  }
  resolution = 3.8
  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=   0.002
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: 5
    Type Number    sf(0)   Gaussians
     S      13      5.16       5
     C    1296      2.51       5
     N     349      2.21       5
     O     354      1.98       5
     H    1958      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3970
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 3970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 3970
          Classifications: {'peptide': 246}
          Link IDs: {'PTRANS': 5, 'TRANS': 240}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 10
  Time building chain proxies: 2.77, per 1000 atoms: 0.70
  Number of scatterers: 3970
  At special positions: 0
  Unit cell: (55.86, 65.66, 104.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      13     16.00
     O     354      8.00
     N     349      7.00
     C    1296      6.00
     H    1958      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.97
  Conformation dependent library (CDL) restraints added in 255.3 milliseconds
  

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  478

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      86.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'B' and resid 5 through 20
    Processing helix  chain 'B' and resid 40 through 51
      removed outlier: 3.518A  pdb=" N   GLU B  44 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   LEU B  49 " --> pdb=" O   GLU B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 105
      removed outlier: 4.154A  pdb=" N   ALA B  91 " --> pdb=" O   VAL B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 107
      No H-bonds generated for 'chain 'B' and resid 106 through 107'
    Processing helix  chain 'B' and resid 111 through 111
      No H-bonds generated for 'chain 'B' and resid 111 through 111'
    Processing helix  chain 'B' and resid 112 through 127
      removed outlier: 4.274A  pdb=" N   GLU B 116 " --> pdb=" O   SER B 112 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   HIS B 117 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 152
      removed outlier: 3.932A  pdb=" N   ASN B 144 " --> pdb=" O   GLN B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 173
      removed outlier: 4.883A  pdb=" N   ALA B 160 " --> pdb=" O   GLU B 156 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   TYR B 161 " --> pdb=" O   THR B 157 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU B 162 " --> pdb=" O   ALA B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 221
      removed outlier: 3.734A  pdb=" N   LEU B 211 " --> pdb=" O   TYR B 207 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ALA B 215 " --> pdb=" O   LEU B 211 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLN B 216 " --> pdb=" O   TYR B 212 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   TYR B 218 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLN B 219 " --> pdb=" O   ALA B 215 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   HIS B 220 " --> pdb=" O   GLN B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 239
      removed outlier: 3.537A  pdb=" N   LEU B 239 " --> pdb=" O   LEU B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 263
      removed outlier: 3.970A  pdb=" N   TRP B 249 " --> pdb=" O   HIS B 245 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ALA B 250 " --> pdb=" O   PRO B 246 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ALA B 254 " --> pdb=" O   ALA B 250 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   SER B 257 " --> pdb=" O   ALA B 253 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   GLN B 258 " --> pdb=" O   ALA B 254 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   PHE B 259 " --> pdb=" O   THR B 255 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   TYR B 260 " --> pdb=" O   LEU B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 281
      removed outlier: 4.148A  pdb=" N   ARG B 270 " --> pdb=" O   PHE B 266 " (cutoff:3.500A)
      removed outlier: 5.038A  pdb=" N   HIS B 271 " --> pdb=" O   MET B 267 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   CYS B 272 " --> pdb=" O   GLU B 268 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LEU B 273 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   VAL B 278 " --> pdb=" O   SER B 274 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ILE B 279 " --> pdb=" O   ALA B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 306
    Processing helix  chain 'B' and resid 307 through 325
      removed outlier: 3.933A  pdb=" N   ALA B 325 " --> pdb=" O   LEU B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 328
      No H-bonds generated for 'chain 'B' and resid 326 through 328'
    Processing helix  chain 'B' and resid 391 through 405
      removed outlier: 4.613A  pdb=" N   VAL B 403 " --> pdb=" O   GLY B 399 " (cutoff:3.500A)

    124 hydrogen bonds defined for protein.
    372 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: 1.11

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        0.40 -     0.69: 2
        0.69 -     0.97: 137
        0.97 -     1.25: 2124
        1.25 -     1.53: 1498
        1.53 -     1.81: 252
  Warning: very small bond lengths.
  Bond restraints: 4013
  Sorted by residual:
  bond pdb=" CG  MET B 267 "
       pdb=" HG2 MET B 267 "
    ideal  model  delta    sigma   weight residual
    0.970  1.583 -0.613 2.00e-02 2.50e+03 9.41e+02
  bond pdb=" N   HIS B 241 "
       pdb=" H   HIS B 241 "
    ideal  model  delta    sigma   weight residual
    0.860  0.404  0.456 2.00e-02 2.50e+03 5.20e+02
  bond pdb=" CB  PHE B 266 "
       pdb=" HB2 PHE B 266 "
    ideal  model  delta    sigma   weight residual
    0.970  0.594  0.376 2.00e-02 2.50e+03 3.53e+02
  bond pdb=" N   LEU B 264 "
       pdb=" H   LEU B 264 "
    ideal  model  delta    sigma   weight residual
    0.860  1.128 -0.268 2.00e-02 2.50e+03 1.80e+02
  bond pdb=" CB  MET B 267 "
       pdb=" HB2 MET B 267 "
    ideal  model  delta    sigma   weight residual
    0.970  0.741  0.229 2.00e-02 2.50e+03 1.31e+02
  ... (remaining 4008 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    13.94: 7162
       13.94 -    27.88: 3
       27.88 -    41.82: 3
       41.82 -    55.77: 0
       55.77 -    69.71: 1
  Bond angle restraints: 7169
  Sorted by residual:
  angle pdb=" HB2 PHE B 266 "
        pdb=" CB  PHE B 266 "
        pdb=" HB3 PHE B 266 "
      ideal   model   delta    sigma   weight residual
     110.00   40.29   69.71 3.00e+00 1.11e-01 5.40e+02
  angle pdb=" CA  PHE B 266 "
        pdb=" CB  PHE B 266 "
        pdb=" HB2 PHE B 266 "
      ideal   model   delta    sigma   weight residual
     109.00   70.58   38.42 3.00e+00 1.11e-01 1.64e+02
  angle pdb=" HG2 MET B 267 "
        pdb=" CG  MET B 267 "
        pdb=" HG3 MET B 267 "
      ideal   model   delta    sigma   weight residual
     110.00  138.24  -28.24 3.00e+00 1.11e-01 8.86e+01
  angle pdb=" CG  PHE B 266 "
        pdb=" CB  PHE B 266 "
        pdb=" HB2 PHE B 266 "
      ideal   model   delta    sigma   weight residual
     108.00  135.95  -27.95 3.00e+00 1.11e-01 8.68e+01
  angle pdb=" SD  MET B 267 "
        pdb=" CG  MET B 267 "
        pdb=" HG2 MET B 267 "
      ideal   model   delta    sigma   weight residual
     108.00   84.32   23.68 3.00e+00 1.11e-01 6.23e+01
  ... (remaining 7164 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.64: 1724
       12.64 -    25.28: 87
       25.28 -    37.92: 43
       37.92 -    50.55: 22
       50.55 -    63.19: 22
  Dihedral angle restraints: 1898
    sinusoidal: 997
      harmonic: 901
  Sorted by residual:
  dihedral pdb=" CA  MET B 223 "
           pdb=" C   MET B 223 "
           pdb=" N   PHE B 224 "
           pdb=" CA  PHE B 224 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.31  -20.69     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" N   PHE B 203 "
           pdb=" CA  PHE B 203 "
           pdb=" CB  PHE B 203 "
           pdb=" CG  PHE B 203 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    0.25   59.75     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  GLN B 400 "
           pdb=" CB  GLN B 400 "
           pdb=" CG  GLN B 400 "
           pdb=" CD  GLN B 400 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -129.95  -50.05     3      1.50e+01 4.44e-03 8.85e+00
  ... (remaining 1895 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 230
       0.057 -    0.114: 60
       0.114 -    0.171: 10
       0.171 -    0.229: 0
       0.229 -    0.286: 1
  Chirality restraints: 301
  Sorted by residual:
  chirality pdb=" CA  ASN B 242 "
            pdb=" N   ASN B 242 "
            pdb=" C   ASN B 242 "
            pdb=" CB  ASN B 242 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.04e+00
  chirality pdb=" CA  PHE B 266 "
            pdb=" N   PHE B 266 "
            pdb=" C   PHE B 266 "
            pdb=" CB  PHE B 266 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.77e-01
  chirality pdb=" CA  VAL B 403 "
            pdb=" N   VAL B 403 "
            pdb=" C   VAL B 403 "
            pdb=" CB  VAL B 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.73e-01
  ... (remaining 298 not shown)

  Planarity restraints: 580
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 242 "    0.304 2.00e-02 2.50e+03   3.43e-01 1.76e+03
        pdb=" CG  ASN B 242 "   -0.023 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 242 "   -0.293 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 242 "   -0.001 2.00e-02 2.50e+03
        pdb="HD21 ASN B 242 "   -0.506 2.00e-02 2.50e+03
        pdb="HD22 ASN B 242 "    0.520 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN B 400 "   -0.184 2.00e-02 2.50e+03   2.10e-01 6.60e+02
        pdb=" CD  GLN B 400 "    0.014 2.00e-02 2.50e+03
        pdb=" OE1 GLN B 400 "    0.175 2.00e-02 2.50e+03
        pdb=" NE2 GLN B 400 "    0.001 2.00e-02 2.50e+03
        pdb="HE21 GLN B 400 "   -0.319 2.00e-02 2.50e+03
        pdb="HE22 GLN B 400 "    0.312 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 262 "   -0.160 2.00e-02 2.50e+03   1.60e-01 3.82e+02
        pdb=" CG  ASN B 262 "    0.012 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 262 "    0.153 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 262 "    0.001 2.00e-02 2.50e+03
        pdb="HD21 ASN B 262 "   -0.230 2.00e-02 2.50e+03
        pdb="HD22 ASN B 262 "    0.225 2.00e-02 2.50e+03
  ... (remaining 577 not shown)

  Histogram of nonbonded interaction distances:
        1.67 -     2.26: 303
        2.26 -     2.84: 7835
        2.84 -     3.43: 9345
        3.43 -     4.01: 11655
        4.01 -     4.60: 17202
  Nonbonded interactions: 46340
  Sorted by model distance:
  nonbonded pdb=" O   LYS B 205 "
            pdb=" HZ2 LYS B 205 "
     model   vdw
     1.674 2.450
  nonbonded pdb=" O   SER B  35 "
            pdb=" H   TYR B  37 "
     model   vdw
     1.680 2.450
  nonbonded pdb=" HA  TYR B 230 "
            pdb=" HD1 TYR B 230 "
     model   vdw
     1.700 2.270
  nonbonded pdb=" O   ALA B 160 "
            pdb=" HG  SER B 164 "
     model   vdw
     1.707 2.450
  nonbonded pdb=" O   LEU B  17 "
            pdb=" HG  SER B  20 "
     model   vdw
     1.727 2.450
  ... (remaining 46335 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             1.140
  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:             0.080
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.470
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6943
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      :  0.008   0.042   2055  Z= 0.502
  Angle     :  0.802   9.818   2768  Z= 0.556
  Chirality :  0.053   0.286    301
  Planarity :  0.004   0.058    345
  Dihedral  : 12.745  59.753    744
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  :  2.40 %
    Favored  : 94.71 %
  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: -0.64 (0.51), residues: 230
  helix: -0.54 (0.34), residues: 169
  sheet:  None (None), residues: 0
  loop :  0.51 (0.87), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B   6 
 HIS   0.002   0.000   HIS B 105 
 PHE   0.013   0.001   PHE B 280 
 TYR   0.010   0.001   TYR B 172 
 ARG   0.003   0.000   ARG B 312 

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

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

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 2
  residues processed: 42
  average time/residue: 0.4352
  time to fit residues: 20.2309
Evaluate side-chains
  24 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  203 PHE
Chi-restraints excluded: chain B residue  265 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 216 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.123415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.109402 restraints weight = 14776.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.112853 restraints weight = 6085.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.114884 restraints weight = 3266.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7046
moved from start:          0.3953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2055  Z= 0.204
  Angle     :  0.551   4.938   2768  Z= 0.309
  Chirality :  0.031   0.116    301
  Planarity :  0.005   0.049    345
  Dihedral  :  5.810  59.599    270
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  5.77 %
    Favored  : 92.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.54), residues: 230
  helix:  0.92 (0.37), residues: 174
  sheet:  None (None), residues: 0
  loop :  0.61 (0.94), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 249 
 HIS   0.004   0.001   HIS B 401 
 PHE   0.014   0.001   PHE B 396 
 TYR   0.018   0.001   TYR B 317 
 ARG   0.008   0.001   ARG B  21 

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

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

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  125 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7861 (tt)
  outliers start: 4
  outliers final: 2
  residues processed: 31
  average time/residue: 0.3271
  time to fit residues: 11.7453
Evaluate side-chains
  25 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 22
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  203 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 4 optimal weight:    0.0050
   chunk 19 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 21 optimal weight:    0.2980
   chunk 18 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.0398

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.118546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.104487 restraints weight = 15011.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.107798 restraints weight = 6162.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.109746 restraints weight = 3316.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.4888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2055  Z= 0.207
  Angle     :  0.510   4.553   2768  Z= 0.288
  Chirality :  0.029   0.096    301
  Planarity :  0.004   0.053    345
  Dihedral  :  5.351  55.661    269
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  9.13 %
    Favored  : 88.94 %
  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:  1.50 (0.56), residues: 230
  helix:  1.49 (0.39), residues: 175
  sheet:  None (None), residues: 0
  loop : -0.45 (0.88), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 249 
 HIS   0.003   0.001   HIS B 105 
 PHE   0.009   0.001   PHE B 396 
 TYR   0.020   0.002   TYR B 317 
 ARG   0.005   0.000   ARG B  21 

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

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

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  125 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7903 (tt)
  outliers start: 4
  outliers final: 1
  residues processed: 25
  average time/residue: 0.2933
  time to fit residues: 8.6337
Evaluate side-chains
  21 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  203 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 4 optimal weight:    0.0670
   chunk 1 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    0.3980
   chunk 21 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.4518

-------------------------------------------------------------------------------
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 = 0.3987 r_free = 0.3987 target = 0.120590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.107057 restraints weight = 14771.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.110317 restraints weight = 6125.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.112297 restraints weight = 3280.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.5249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   2055  Z= 0.145
  Angle     :  0.450   4.560   2768  Z= 0.244
  Chirality :  0.028   0.112    301
  Planarity :  0.004   0.057    345
  Dihedral  :  5.207  57.595    269
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 1.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 11.54 %
    Favored  : 87.02 %
  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:  2.23 (0.57), residues: 230
  helix:  2.20 (0.40), residues: 168
  sheet:  None (None), residues: 0
  loop : -0.56 (0.83), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 149 
 HIS   0.002   0.000   HIS B 105 
 PHE   0.010   0.001   PHE B 396 
 TYR   0.011   0.001   TYR B 317 
 ARG   0.008   0.001   ARG B  21 

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

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

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 19
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  125 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7810 (tt)
  outliers start: 3
  outliers final: 1
  residues processed: 21
  average time/residue: 0.3365
  time to fit residues: 8.3641
Evaluate side-chains
  21 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 19
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  203 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 18 optimal weight:    0.2980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.118402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.104220 restraints weight = 15353.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.107516 restraints weight = 6340.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.109611 restraints weight = 3433.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.5586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   2055  Z= 0.163
  Angle     :  0.435   4.165   2768  Z= 0.238
  Chirality :  0.028   0.090    301
  Planarity :  0.004   0.050    345
  Dihedral  :  5.109  56.109    269
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 1.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 12.50 %
    Favored  : 85.58 %
  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:  2.07 (0.57), residues: 230
  helix:  1.88 (0.40), residues: 186
  sheet:  None (None), residues: 0
  loop : -0.78 (0.90), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B 314 
 HIS   0.003   0.001   HIS B 105 
 PHE   0.007   0.001   PHE B 396 
 TYR   0.015   0.001   TYR B 317 
 ARG   0.004   0.000   ARG B  21 

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

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

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 17
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 19
  average time/residue: 0.3706
  time to fit residues: 8.2131
Evaluate side-chains
  19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  203 PHE
Chi-restraints excluded: chain B residue  397 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0270
   chunk 5 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.7238

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.116445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.101925 restraints weight = 16129.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.105217 restraints weight = 6786.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.107279 restraints weight = 3714.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.5916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   2055  Z= 0.164
  Angle     :  0.434   3.898   2768  Z= 0.238
  Chirality :  0.027   0.088    301
  Planarity :  0.004   0.068    345
  Dihedral  :  5.059  55.772    269
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 1.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 14.42 %
    Favored  : 85.10 %
  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:  2.24 (0.58), residues: 230
  helix:  2.07 (0.40), residues: 186
  sheet:  None (None), residues: 0
  loop : -1.10 (0.84), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B   6 
 HIS   0.002   0.001   HIS B 105 
 PHE   0.015   0.001   PHE B 396 
 TYR   0.015   0.001   TYR B 317 
 ARG   0.005   0.000   ARG B  21 

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

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

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 17
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 18
  average time/residue: 0.3574
  time to fit residues: 7.5897
Evaluate side-chains
  15 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 14
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  203 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.115778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.100856 restraints weight = 16610.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.104148 restraints weight = 7020.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.106151 restraints weight = 3860.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7093
moved from start:          0.6102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   2055  Z= 0.162
  Angle     :  0.446   4.124   2768  Z= 0.238
  Chirality :  0.027   0.088    301
  Planarity :  0.003   0.033    345
  Dihedral  :  5.023  55.951    269
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 12.98 %
    Favored  : 85.10 %
  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:  2.24 (0.58), residues: 230
  helix:  2.05 (0.40), residues: 190
  sheet:  None (None), residues: 0
  loop : -1.37 (0.81), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B 314 
 HIS   0.002   0.001   HIS B 105 
 PHE   0.012   0.001   PHE B 396 
 TYR   0.014   0.001   TYR B 317 
 ARG   0.003   0.000   ARG B  21 

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

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

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   21 ARG cc_start: 0.8844 (tpp80) cc_final: 0.8639 (mmm160)
  outliers start: 4
  outliers final: 4
  residues processed: 19
  average time/residue: 0.3396
  time to fit residues: 7.5887
Evaluate side-chains
  19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 15
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  203 PHE
Chi-restraints excluded: chain B residue  397 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 20 optimal weight:    0.4980
   chunk 7 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.116018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.101318 restraints weight = 15518.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.104601 restraints weight = 6441.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.106647 restraints weight = 3524.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7082
moved from start:          0.6241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   2055  Z= 0.152
  Angle     :  0.426   4.045   2768  Z= 0.229
  Chirality :  0.027   0.087    301
  Planarity :  0.002   0.021    345
  Dihedral  :  4.995  56.260    269
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.50 %
    Favored  : 86.06 %
  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:  2.29 (0.58), residues: 230
  helix:  2.10 (0.40), residues: 190
  sheet:  None (None), residues: 0
  loop : -1.44 (0.77), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 249 
 HIS   0.002   0.001   HIS B 105 
 PHE   0.006   0.001   PHE B 396 
 TYR   0.014   0.001   TYR B 317 
 ARG   0.002   0.000   ARG B  21 

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

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

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 20
  average time/residue: 0.3379
  time to fit residues: 7.9309
Evaluate side-chains
  18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 16
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  203 PHE
Chi-restraints excluded: chain B residue  397 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.114695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.100128 restraints weight = 15922.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.103433 restraints weight = 6683.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.105424 restraints weight = 3652.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.6320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2055  Z= 0.189
  Angle     :  0.463   4.217   2768  Z= 0.250
  Chirality :  0.027   0.094    301
  Planarity :  0.006   0.095    345
  Dihedral  :  5.134  54.897    269
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 13.94 %
    Favored  : 85.10 %
  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:  2.14 (0.58), residues: 230
  helix:  2.02 (0.40), residues: 190
  sheet:  None (None), residues: 0
  loop : -1.60 (0.77), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 314 
 HIS   0.003   0.001   HIS B 105 
 PHE   0.015   0.001   PHE B 396 
 TYR   0.017   0.001   TYR B 317 
 ARG   0.016   0.001   ARG B  21 

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

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

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 19
  average time/residue: 0.3434
  time to fit residues: 7.6939
Evaluate side-chains
  18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 16
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  203 PHE
Chi-restraints excluded: chain B residue  397 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 3 optimal weight:    0.3980
   chunk 5 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.115443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.100650 restraints weight = 15833.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.103960 restraints weight = 6708.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.106040 restraints weight = 3695.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.6414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   2055  Z= 0.152
  Angle     :  0.441   4.197   2768  Z= 0.234
  Chirality :  0.027   0.087    301
  Planarity :  0.002   0.021    345
  Dihedral  :  5.062  55.888    269
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 13.46 %
    Favored  : 85.10 %
  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:  2.32 (0.58), residues: 230
  helix:  2.26 (0.41), residues: 185
  sheet:  None (None), residues: 0
  loop : -1.70 (0.71), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 314 
 HIS   0.002   0.001   HIS B 105 
 PHE   0.013   0.001   PHE B 396 
 TYR   0.013   0.001   TYR B 317 
 ARG   0.001   0.000   ARG B 312 

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

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

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  460 Ramachandran restraints generated.
    230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 20
  average time/residue: 0.3319
  time to fit residues: 7.8744
Evaluate side-chains
  18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 16
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  203 PHE
Chi-restraints excluded: chain B residue  397 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0980
   chunk 23 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0470
   chunk 22 optimal weight:    0.4980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.116608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.102247 restraints weight = 15578.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.105455 restraints weight = 6756.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.107430 restraints weight = 3762.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
moved from start:          0.6570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2055  Z= 0.137
  Angle     :  0.420   4.214   2768  Z= 0.220
  Chirality :  0.026   0.084    301
  Planarity :  0.002   0.022    345
  Dihedral  :  4.914  57.076    269
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 2.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 14.42 %
    Favored  : 84.62 %
  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:  2.61 (0.58), residues: 230
  helix:  2.48 (0.41), residues: 186
  sheet:  None (None), residues: 0
  loop : -1.76 (0.68), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B 249 
 HIS   0.002   0.000   HIS B 105 
 PHE   0.012   0.001   PHE B 396 
 TYR   0.011   0.001   TYR B 244 
 ARG   0.001   0.000   ARG B  21 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2028.57 seconds
wall clock time: 35 minutes 11.46 seconds (2111.46 seconds total)