Starting phenix.real_space_refine
on Tue Mar  3 12:12:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rsq_24677/03_2026/7rsq_24677.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rsq_24677/03_2026/7rsq_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rsq_24677/03_2026/7rsq_24677.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rsq_24677/03_2026/7rsq_24677.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rsq_24677/03_2026/7rsq_24677.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rsq_24677/03_2026/7rsq_24677.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.77, per 1000 atoms: 0.19
  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: 0.32
  Conformation dependent library (CDL) restraints added in 84.7 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: 0.09
  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: 0.71

  Time building geometry restraints manager: 0.43 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:             1.860
  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:             0.020
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     5.480
  Find NCS groups from input model:        0.010
  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:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.940
-------------------------------------------------------------------------------
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= 0.430
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.003   0.000   ARG B 312 
 TYR   0.010   0.001   TYR B 172 
 PHE   0.013   0.001   PHE B 280 
 TRP   0.001   0.000   TRP B   6 
 HIS   0.002   0.000   HIS B 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00782 ( 2055)
  covalent geometry    : angle       0.80246 ( 2768)
  hydrogen bonds       : bond        0.27995 (  124)
  hydrogen bonds       : angle       7.09674 (  372)

*********************** 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  : 0.106 
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: 0.2079
  time to fit residues: 9.5312
Evaluate side-chains
  25 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 23
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
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 12 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 4 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 = 0.4038 r_free = 0.4038 target = 0.125163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.111124 restraints weight = 14328.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.114614 restraints weight = 5906.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.116759 restraints weight = 3146.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.117955 restraints weight = 1962.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.118596 restraints weight = 1427.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6974
moved from start:          0.4043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2055  Z= 0.163
  Angle     :  0.561   4.303   2768  Z= 0.311
  Chirality :  0.031   0.121    301
  Planarity :  0.005   0.050    345
  Dihedral  :  5.825  59.720    270
  Min Nonbonded Distance : 2.479

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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.19 (0.53), residues: 230
  helix:  1.05 (0.37), residues: 169
  sheet:  None (None), residues: 0
  loop :  0.34 (0.87), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  21 
 TYR   0.019   0.001   TYR B 317 
 PHE   0.015   0.002   PHE B 396 
 TRP   0.007   0.001   TRP B 249 
 HIS   0.004   0.001   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 2055)
  covalent geometry    : angle       0.56137 ( 2768)
  hydrogen bonds       : bond        0.06710 (  124)
  hydrogen bonds       : angle       4.77414 (  372)

*********************** 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  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 GLU cc_start: 0.8508 (mp0) cc_final: 0.8207 (mp0)
REVERT: B  125 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7830 (tt)
  outliers start: 4
  outliers final: 2
  residues processed: 31
  average time/residue: 0.1251
  time to fit residues: 4.4535
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  : 0.077 
-------------------------------------------------------------------------------
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 18 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3964 r_free = 0.3964 target = 0.119963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.105532 restraints weight = 15621.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.108921 restraints weight = 6559.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.110919 restraints weight = 3561.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.112262 restraints weight = 2299.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.113083 restraints weight = 1648.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.4855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2055  Z= 0.144
  Angle     :  0.490   6.360   2768  Z= 0.272
  Chirality :  0.028   0.094    301
  Planarity :  0.004   0.048    345
  Dihedral  :  5.247  57.030    269
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 1.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.72 (0.56), residues: 230
  helix:  1.66 (0.39), residues: 175
  sheet:  None (None), residues: 0
  loop : -0.47 (0.85), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  21 
 TYR   0.018   0.001   TYR B 317 
 PHE   0.009   0.001   PHE B 396 
 TRP   0.005   0.001   TRP B 249 
 HIS   0.002   0.001   HIS B 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 2055)
  covalent geometry    : angle       0.49003 ( 2768)
  hydrogen bonds       : bond        0.05936 (  124)
  hydrogen bonds       : angle       4.37253 (  372)

*********************** 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  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  125 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7844 (tt)
  outliers start: 3
  outliers final: 1
  residues processed: 25
  average time/residue: 0.1647
  time to fit residues: 4.7104
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  : 0.105 
-------------------------------------------------------------------------------
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 1 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.118564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.104879 restraints weight = 14961.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.108126 restraints weight = 6317.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.110110 restraints weight = 3442.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.111291 restraints weight = 2184.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.112074 restraints weight = 1585.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.5364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   2055  Z= 0.139
  Angle     :  0.471   5.285   2768  Z= 0.260
  Chirality :  0.029   0.094    301
  Planarity :  0.004   0.057    345
  Dihedral  :  5.216  55.873    269
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 1.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.67 (0.55), residues: 230
  helix:  1.81 (0.39), residues: 176
  sheet:  None (None), residues: 0
  loop : -1.24 (0.75), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  21 
 TYR   0.017   0.001   TYR B 317 
 PHE   0.009   0.001   PHE B 396 
 TRP   0.004   0.001   TRP B 249 
 HIS   0.003   0.001   HIS B 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 2055)
  covalent geometry    : angle       0.47080 ( 2768)
  hydrogen bonds       : bond        0.05542 (  124)
  hydrogen bonds       : angle       4.24691 (  372)

*********************** 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: 4
    poor density    : 18
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  125 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7833 (tt)
  outliers start: 4
  outliers final: 1
  residues processed: 21
  average time/residue: 0.1463
  time to fit residues: 3.5800
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  : 0.130 
-------------------------------------------------------------------------------
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 10 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0470
   chunk 18 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.7080

-------------------------------------------------------------------------------
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 = 0.3936 r_free = 0.3936 target = 0.117926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.103734 restraints weight = 15499.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.107142 restraints weight = 6404.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.109209 restraints weight = 3418.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.110428 restraints weight = 2171.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.111125 restraints weight = 1571.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7072
moved from start:          0.5748

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= 0.118
  Angle     :  0.431   3.698   2768  Z= 0.238
  Chirality :  0.027   0.089    301
  Planarity :  0.004   0.057    345
  Dihedral  :  5.078  55.867    269
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 1.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 11.06 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.57), residues: 230
  helix:  2.00 (0.40), residues: 181
  sheet:  None (None), residues: 0
  loop : -1.47 (0.80), residues: 49

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  21 
 TYR   0.015   0.001   TYR B 317 
 PHE   0.008   0.001   PHE B 396 
 TRP   0.002   0.001   TRP B   6 
 HIS   0.003   0.001   HIS B 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 2055)
  covalent geometry    : angle       0.43104 ( 2768)
  hydrogen bonds       : bond        0.04846 (  124)
  hydrogen bonds       : angle       3.99270 (  372)

*********************** 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
  22 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 17
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 3
  residues processed: 19
  average time/residue: 0.1566
  time to fit residues: 3.4311
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  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 LEU
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 4 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    1.1786

-------------------------------------------------------------------------------
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 = 0.3868 r_free = 0.3868 target = 0.113935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.099513 restraints weight = 16315.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.102723 restraints weight = 6927.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.104640 restraints weight = 3842.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.105987 restraints weight = 2519.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.106694 restraints weight = 1815.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
moved from start:          0.6032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   2055  Z= 0.165
  Angle     :  0.499   3.751   2768  Z= 0.282
  Chirality :  0.029   0.095    301
  Planarity :  0.005   0.068    345
  Dihedral  :  5.234  52.981    269
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 12.98 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.56), residues: 230
  helix:  1.57 (0.39), residues: 186
  sheet:  None (None), residues: 0
  loop : -1.63 (0.82), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  21 
 TYR   0.022   0.002   TYR B 317 
 PHE   0.018   0.002   PHE B 396 
 TRP   0.006   0.001   TRP B 249 
 HIS   0.004   0.001   HIS B 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 2055)
  covalent geometry    : angle       0.49896 ( 2768)
  hydrogen bonds       : bond        0.06305 (  124)
  hydrogen bonds       : angle       4.31848 (  372)

*********************** 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
  22 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 17
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 21
  average time/residue: 0.1381
  time to fit residues: 3.4157
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  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  203 PHE
Chi-restraints excluded: chain B residue  244 TYR
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 5 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0010
   chunk 22 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 17 optimal weight:    0.4980
   overall best weight:    0.5186

-------------------------------------------------------------------------------
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 = 0.3905 r_free = 0.3905 target = 0.116430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.102027 restraints weight = 16214.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.105331 restraints weight = 6827.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.107304 restraints weight = 3737.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.108613 restraints weight = 2424.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.109398 restraints weight = 1758.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.6208

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= 0.105
  Angle     :  0.421   3.636   2768  Z= 0.230
  Chirality :  0.027   0.088    301
  Planarity :  0.004   0.050    345
  Dihedral  :  5.075  55.186    269
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 2.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.93 (0.58), residues: 230
  helix:  1.84 (0.40), residues: 191
  sheet:  None (None), residues: 0
  loop : -1.55 (0.82), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  21 
 TYR   0.012   0.001   TYR B 317 
 PHE   0.011   0.001   PHE B 396 
 TRP   0.001   0.000   TRP B 149 
 HIS   0.002   0.001   HIS B 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 2055)
  covalent geometry    : angle       0.42095 ( 2768)
  hydrogen bonds       : bond        0.04634 (  124)
  hydrogen bonds       : angle       3.86538 (  372)

*********************** 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  : 0.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 4
  residues processed: 20
  average time/residue: 0.1492
  time to fit residues: 3.4907
Evaluate side-chains
  18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 14
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
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  240 GLU
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 9 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   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 = 0.3884 r_free = 0.3884 target = 0.115021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.100648 restraints weight = 16018.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.103898 restraints weight = 6785.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.105926 restraints weight = 3745.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.107107 restraints weight = 2411.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.107965 restraints weight = 1773.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.6378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2055  Z= 0.128
  Angle     :  0.446   3.681   2768  Z= 0.244
  Chirality :  0.027   0.093    301
  Planarity :  0.004   0.052    345
  Dihedral  :  5.045  54.124    269
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 1.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 12.02 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.58), residues: 230
  helix:  1.75 (0.40), residues: 191
  sheet:  None (None), residues: 0
  loop : -1.77 (0.79), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  21 
 TYR   0.016   0.001   TYR B 317 
 PHE   0.007   0.001   PHE B 396 
 TRP   0.002   0.001   TRP B 314 
 HIS   0.003   0.001   HIS B 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 2055)
  covalent geometry    : angle       0.44565 ( 2768)
  hydrogen bonds       : bond        0.05129 (  124)
  hydrogen bonds       : angle       3.96769 (  372)

*********************** 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: 5
    poor density    : 15
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 20
  average time/residue: 0.1609
  time to fit residues: 3.7121
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  : 0.105 
-------------------------------------------------------------------------------
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  240 GLU
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 10 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0470
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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 = 0.116559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.102169 restraints weight = 16058.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.105493 restraints weight = 6725.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.107518 restraints weight = 3672.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.108828 restraints weight = 2352.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.109696 restraints weight = 1688.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          0.6501

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= 0.105
  Angle     :  0.420   3.569   2768  Z= 0.225
  Chirality :  0.026   0.085    301
  Planarity :  0.004   0.054    345
  Dihedral  :  4.969  54.997    269
  Min Nonbonded Distance : 2.523

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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.07 (0.58), residues: 230
  helix:  2.10 (0.41), residues: 186
  sheet:  None (None), residues: 0
  loop : -1.95 (0.73), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  21 
 TYR   0.012   0.001   TYR B 317 
 PHE   0.008   0.001   PHE B 396 
 TRP   0.001   0.000   TRP B 314 
 HIS   0.002   0.001   HIS B 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 2055)
  covalent geometry    : angle       0.41957 ( 2768)
  hydrogen bonds       : bond        0.04342 (  124)
  hydrogen bonds       : angle       3.73678 (  372)

*********************** 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
  20 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   21 ARG cc_start: 0.8422 (mmm160) cc_final: 0.8202 (tpp80)
  outliers start: 4
  outliers final: 2
  residues processed: 20
  average time/residue: 0.1460
  time to fit residues: 3.4096
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  : 0.067 
-------------------------------------------------------------------------------
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 20 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 16 optimal weight:    0.4980
   chunk 2 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.115857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.101580 restraints weight = 15448.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.104820 restraints weight = 6449.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.106828 restraints weight = 3542.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.108032 restraints weight = 2282.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.108913 restraints weight = 1672.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.6543

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= 0.117
  Angle     :  0.439   3.581   2768  Z= 0.238
  Chirality :  0.027   0.091    301
  Planarity :  0.004   0.053    345
  Dihedral  :  4.966  54.464    269
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 1.50
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.58), residues: 230
  helix:  2.05 (0.41), residues: 186
  sheet:  None (None), residues: 0
  loop : -1.98 (0.73), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  21 
 TYR   0.015   0.001   TYR B 317 
 PHE   0.013   0.001   PHE B 396 
 TRP   0.002   0.000   TRP B 314 
 HIS   0.003   0.001   HIS B 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 2055)
  covalent geometry    : angle       0.43934 ( 2768)
  hydrogen bonds       : bond        0.04796 (  124)
  hydrogen bonds       : angle       3.83185 (  372)

********************** 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
  18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 16
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 18
  average time/residue: 0.1603
  time to fit residues: 3.3261
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  : 0.096 
-------------------------------------------------------------------------------
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 21 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 15 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 2 optimal weight:    0.3980
   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 = 0.3894 r_free = 0.3894 target = 0.115934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.101435 restraints weight = 15958.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.104733 restraints weight = 6790.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.106662 restraints weight = 3741.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.107963 restraints weight = 2445.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.108755 restraints weight = 1775.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7128
moved from start:          0.6596

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= 0.114
  Angle     :  0.454   6.028   2768  Z= 0.243
  Chirality :  0.027   0.088    301
  Planarity :  0.002   0.022    345
  Dihedral  :  4.950  54.571    269
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 1.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.04 (0.58), residues: 230
  helix:  2.09 (0.40), residues: 186
  sheet:  None (None), residues: 0
  loop : -2.01 (0.73), residues: 44

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  21 
 TYR   0.014   0.001   TYR B 317 
 PHE   0.013   0.001   PHE B 396 
 TRP   0.002   0.000   TRP B 314 
 HIS   0.002   0.001   HIS B 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 2055)
  covalent geometry    : angle       0.45362 ( 2768)
  hydrogen bonds       : bond        0.04608 (  124)
  hydrogen bonds       : angle       3.76955 (  372)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1104.96 seconds
wall clock time: 19 minutes 21.17 seconds (1161.17 seconds total)