Starting phenix.real_space_refine
on Tue Feb 11 03:36:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rsq_24677/02_2025/7rsq_24677.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rsq_24677/02_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_24677/02_2025/7rsq_24677.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rsq_24677/02_2025/7rsq_24677.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rsq_24677/02_2025/7rsq_24677.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rsq_24677/02_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-5592/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: 3.03, per 1000 atoms: 0.76
  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: 1.07
  Conformation dependent library (CDL) restraints added in 284.5 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: 0.31
  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: 1.12

  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:
        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:             1.470
  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:             0.070
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.960
  Find NCS groups from input model:        0.020
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.610
-------------------------------------------------------------------------------
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  : 0.299 
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: 0.4386
  time to fit residues: 20.3339
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  : 0.329 
-------------------------------------------------------------------------------
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:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4034 r_free = 0.4034 target = 0.124865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.110838 restraints weight = 14582.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.114304 restraints weight = 6143.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.116382 restraints weight = 3317.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.3990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   2055  Z= 0.199
  Angle     :  0.554   4.335   2768  Z= 0.307
  Chirality :  0.031   0.119    301
  Planarity :  0.005   0.047    345
  Dihedral  :  5.826  59.873    270
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  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:  1.51 (0.54), residues: 230
  helix:  1.27 (0.37), residues: 163
  sheet:  None (None), residues: 0
  loop :  0.59 (0.87), residues: 67

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   0.016   0.002   PHE B 396 
 TYR   0.019   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  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  125 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7847 (tt)
  outliers start: 4
  outliers final: 2
  residues processed: 31
  average time/residue: 0.3163
  time to fit residues: 11.3041
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  : 0.305 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 19 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 21 optimal weight:    0.4980
   chunk 18 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.3991 r_free = 0.3991 target = 0.121029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.107171 restraints weight = 14906.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.110489 restraints weight = 6132.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.112436 restraints weight = 3288.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.4763

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= 0.172
  Angle     :  0.480   4.710   2768  Z= 0.267
  Chirality :  0.029   0.114    301
  Planarity :  0.004   0.051    345
  Dihedral  :  5.268  58.213    269
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 2.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  9.62 %
    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:  1.82 (0.56), residues: 230
  helix:  1.68 (0.39), residues: 175
  sheet:  None (None), residues: 0
  loop : -0.21 (0.89), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 249 
 HIS   0.002   0.001   HIS B 105 
 PHE   0.009   0.001   PHE B 396 
 TYR   0.016   0.001   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: 3
    poor density    : 23
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  125 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7850 (tt)
  outliers start: 3
  outliers final: 1
  residues processed: 25
  average time/residue: 0.3015
  time to fit residues: 9.0086
Evaluate side-chains
  23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 21
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
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:    0.0040
   chunk 1 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0970
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.4190

-------------------------------------------------------------------------------
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 = 0.3988 r_free = 0.3988 target = 0.120860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.106987 restraints weight = 15229.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.110302 restraints weight = 6216.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.112369 restraints weight = 3346.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6996
moved from start:          0.5197

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= 0.149
  Angle     :  0.447   5.138   2768  Z= 0.243
  Chirality :  0.027   0.093    301
  Planarity :  0.004   0.056    345
  Dihedral  :  5.157  58.862    269
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 1.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 12.50 %
    Favored  : 86.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.57), residues: 230
  helix:  2.34 (0.40), residues: 168
  sheet:  None (None), residues: 0
  loop : -0.40 (0.83), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 149 
 HIS   0.002   0.001   HIS B 245 
 PHE   0.009   0.001   PHE B 396 
 TYR   0.011   0.001   TYR B 317 
 ARG   0.006   0.000   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: 2
    poor density    : 20
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  125 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7740 (tt)
  outliers start: 2
  outliers final: 1
  residues processed: 21
  average time/residue: 0.3334
  time to fit residues: 8.2444
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  : 0.368 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0970
   chunk 16 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 = 0.3981 r_free = 0.3981 target = 0.120560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.106351 restraints weight = 15284.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.109744 restraints weight = 6305.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.111731 restraints weight = 3390.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.5510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2055  Z= 0.146
  Angle     :  0.417   4.143   2768  Z= 0.227
  Chirality :  0.027   0.089    301
  Planarity :  0.004   0.055    345
  Dihedral  :  5.019  57.890    269
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 2.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 12.02 %
    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:  2.45 (0.57), residues: 230
  helix:  2.33 (0.40), residues: 178
  sheet:  None (None), residues: 0
  loop : -0.98 (0.81), residues: 52

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   0.006   0.001   PHE B 396 
 TYR   0.014   0.001   TYR B 317 
 ARG   0.007   0.001   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
  23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  125 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7694 (tt)
  outliers start: 4
  outliers final: 1
  residues processed: 21
  average time/residue: 0.3372
  time to fit residues: 8.3268
Evaluate side-chains
  20 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 18
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  203 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
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:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 2 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3919 r_free = 0.3919 target = 0.116982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.102389 restraints weight = 16273.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.105708 restraints weight = 6873.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.107713 restraints weight = 3772.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.5813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2055  Z= 0.171
  Angle     :  0.445   3.831   2768  Z= 0.245
  Chirality :  0.028   0.090    301
  Planarity :  0.004   0.067    345
  Dihedral  :  5.052  56.359    269
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 2.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 13.94 %
    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:  2.33 (0.57), residues: 230
  helix:  2.09 (0.40), residues: 186
  sheet:  None (None), residues: 0
  loop : -0.87 (0.84), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 249 
 HIS   0.003   0.001   HIS B 105 
 PHE   0.016   0.002   PHE B 396 
 TYR   0.018   0.001   TYR B 317 
 ARG   0.007   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
  21 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 18
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  125 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7700 (tt)
  outliers start: 3
  outliers final: 2
  residues processed: 20
  average time/residue: 0.4045
  time to fit residues: 9.6169
Evaluate side-chains
  19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 16
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 3 optimal weight:    0.0870
   chunk 11 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0980
   chunk 15 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.4558

-------------------------------------------------------------------------------
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 = 0.3926 r_free = 0.3926 target = 0.117974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.103043 restraints weight = 16569.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.106468 restraints weight = 6989.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.108540 restraints weight = 3795.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7027
moved from start:          0.6000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   2055  Z= 0.133
  Angle     :  0.420   4.191   2768  Z= 0.223
  Chirality :  0.026   0.086    301
  Planarity :  0.002   0.026    345
  Dihedral  :  4.965  57.889    269
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  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:  2.81 (0.59), residues: 230
  helix:  2.48 (0.41), residues: 183
  sheet:  None (None), residues: 0
  loop : -0.72 (0.90), residues: 47

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 314 
 HIS   0.002   0.000   HIS B 105 
 PHE   0.012   0.001   PHE B 396 
 TYR   0.011   0.001   TYR B 317 
 ARG   0.001   0.000   ARG B 312 

*********************** 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  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 3
  residues processed: 19
  average time/residue: 0.3476
  time to fit residues: 7.7571
Evaluate side-chains
  19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 16
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  122 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:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.115254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.100462 restraints weight = 15820.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.103775 restraints weight = 6722.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.105811 restraints weight = 3703.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.6161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2055  Z= 0.182
  Angle     :  0.458   3.948   2768  Z= 0.250
  Chirality :  0.027   0.094    301
  Planarity :  0.002   0.019    345
  Dihedral  :  5.033  56.000    269
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 13.94 %
    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:  2.20 (0.58), residues: 230
  helix:  2.02 (0.40), residues: 190
  sheet:  None (None), residues: 0
  loop : -1.32 (0.82), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 249 
 HIS   0.002   0.001   HIS B 105 
 PHE   0.013   0.002   PHE B 396 
 TYR   0.018   0.001   TYR B 317 
 ARG   0.001   0.000   ARG B 126 

*********************** 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  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 19
  average time/residue: 0.3385
  time to fit residues: 7.5601
Evaluate side-chains
  18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 15
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=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:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 19 optimal weight:    0.2980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3902 r_free = 0.3902 target = 0.116096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.101308 restraints weight = 15700.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.104660 restraints weight = 6653.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.106738 restraints weight = 3654.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.6286

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     :  0.446   4.033   2768  Z= 0.239
  Chirality :  0.027   0.088    301
  Planarity :  0.002   0.020    345
  Dihedral  :  5.060  56.423    269
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 12.98 %
    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:  2.18 (0.58), residues: 230
  helix:  2.04 (0.40), residues: 190
  sheet:  None (None), residues: 0
  loop : -1.53 (0.80), residues: 40

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B   6 
 HIS   0.003   0.001   HIS B 105 
 PHE   0.008   0.001   PHE B 396 
 TYR   0.015   0.001   TYR B 317 
 ARG   0.001   0.000   ARG B 393 

*********************** 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  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 19
  average time/residue: 0.3654
  time to fit residues: 8.1384
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  : 0.315 
-------------------------------------------------------------------------------
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:    0.0570
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.6298

-------------------------------------------------------------------------------
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 = 0.3900 r_free = 0.3900 target = 0.116162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.101230 restraints weight = 15657.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.104617 restraints weight = 6520.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.106651 restraints weight = 3571.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.6368

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= 0.154
  Angle     :  0.440   4.233   2768  Z= 0.233
  Chirality :  0.027   0.087    301
  Planarity :  0.002   0.020    345
  Dihedral  :  5.055  56.817    269
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 12.98 %
    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:  2.26 (0.58), residues: 230
  helix:  2.14 (0.40), residues: 191
  sheet:  None (None), residues: 0
  loop : -1.84 (0.75), residues: 39

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   0.008   0.001   PHE B 396 
 TYR   0.014   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
  19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 17
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 19
  average time/residue: 0.3588
  time to fit residues: 8.0003
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  : 0.342 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0670
   chunk 23 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 9 optimal weight:    0.1980
   chunk 18 optimal weight:    0.5980
   chunk 22 optimal weight:    0.3980
   chunk 12 optimal weight:    0.0270
   overall best weight:    0.2576

-------------------------------------------------------------------------------
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 = 0.3939 r_free = 0.3939 target = 0.119060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.104275 restraints weight = 15520.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.107669 restraints weight = 6542.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.109687 restraints weight = 3604.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.6546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   2055  Z= 0.125
  Angle     :  0.410   4.255   2768  Z= 0.211
  Chirality :  0.026   0.083    301
  Planarity :  0.002   0.021    345
  Dihedral  :  4.892  58.718    269
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 1.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  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:  2.96 (0.59), residues: 230
  helix:  2.86 (0.41), residues: 179
  sheet:  None (None), residues: 0
  loop : -1.59 (0.78), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B 249 
 HIS   0.002   0.000   HIS B 245 
 PHE   0.012   0.001   PHE B 396 
 TYR   0.008   0.001   TYR B 317 
 ARG   0.002   0.000   ARG B  21 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1968.31 seconds
wall clock time: 35 minutes 23.62 seconds (2123.62 seconds total)