Starting phenix.real_space_refine
on Fri Aug 22 16:16:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jo4_36455/08_2025/8jo4_36455_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jo4_36455/08_2025/8jo4_36455.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jo4_36455/08_2025/8jo4_36455.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jo4_36455/08_2025/8jo4_36455.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jo4_36455/08_2025/8jo4_36455_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jo4_36455/08_2025/8jo4_36455_neut.cif"
  }
  resolution = 3.04
  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=  -0.001 sd=   0.078
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: 7
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     P       6      5.49       5
     Mg      1      5.21       5
     S      27      5.16       5
     C    3616      2.51       5
     N     951      2.21       5
     O    1117      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5719
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2846
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 2846
          Classifications: {'peptide': 350}
          Link IDs: {'PTRANS': 11, 'TRANS': 338}
    Chain: "B"
      Number of atoms: 2809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 359, 2809
          Classifications: {'peptide': 359}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 339}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' CA': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.37, per 1000 atoms: 0.24
  Number of scatterers: 5719
  At special positions: 0
  Unit cell: (64.17, 80.91, 113.46, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Ca      1     19.99
     S      27     16.00
     P       6     15.00
     Mg      1     11.99
     O    1117      8.00
     N     951      7.00
     C    3616      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.38
  Conformation dependent library (CDL) restraints added in 226.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1348

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 7 sheets defined
      59.8% alpha, 9.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 15
    Processing helix  chain 'A' and resid 20 through 36
    Processing helix  chain 'A' and resid 41 through 55
      removed outlier: 3.659A  pdb=" N   PHE A  45 " --> pdb=" O   ASN A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 72
    Processing helix  chain 'A' and resid 72 through 77
    Processing helix  chain 'A' and resid 77 through 89
      removed outlier: 3.693A  pdb=" N   SER A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 118
    Processing helix  chain 'A' and resid 121 through 134
      removed outlier: 4.226A  pdb=" N   PHE A 125 " --> pdb=" O   ASP A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 160
    Processing helix  chain 'A' and resid 161 through 164
    Processing helix  chain 'A' and resid 168 through 175
    Processing helix  chain 'A' and resid 177 through 181
    Processing helix  chain 'A' and resid 228 through 233
    Processing helix  chain 'A' and resid 244 through 259
      removed outlier: 3.795A  pdb=" N   SER A 248 " --> pdb=" O   GLY A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 284
    Processing helix  chain 'A' and resid 288 through 297
      removed outlier: 3.552A  pdb=" N   VAL A 292 " --> pdb=" O   SER A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 308
      removed outlier: 3.660A  pdb=" N   ALA A 308 " --> pdb=" O   ILE A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 352
    Processing helix  chain 'B' and resid 57 through 63
    Processing helix  chain 'B' and resid 80 through 93
    Processing helix  chain 'B' and resid 99 through 103
    Processing helix  chain 'B' and resid 114 through 128
    Processing helix  chain 'B' and resid 139 through 147
      removed outlier: 3.782A  pdb=" N   SER B 147 " --> pdb=" O   SER B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 198
    Processing helix  chain 'B' and resid 204 through 218
    Processing helix  chain 'B' and resid 224 through 235
    Processing helix  chain 'B' and resid 254 through 262
      removed outlier: 3.548A  pdb=" N   CYS B 259 " --> pdb=" O   GLU B 255 " (cutoff:3.500A)
      Proline residue:  B 260  - end of helix
    Processing helix  chain 'B' and resid 263 through 264
      No H-bonds generated for 'chain 'B' and resid 263 through 264'
    Processing helix  chain 'B' and resid 265 through 270
    Processing helix  chain 'B' and resid 275 through 286
    Processing helix  chain 'B' and resid 291 through 298
    Processing helix  chain 'B' and resid 303 through 307
    Processing helix  chain 'B' and resid 310 through 323
    Processing helix  chain 'B' and resid 336 through 338
      No H-bonds generated for 'chain 'B' and resid 336 through 338'
    Processing helix  chain 'B' and resid 339 through 350
    Processing helix  chain 'B' and resid 352 through 357
      removed outlier: 3.908A  pdb=" N   GLN B 356 " --> pdb=" O   THR B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 368
    Processing helix  chain 'B' and resid 370 through 376
      removed outlier: 3.728A  pdb=" N   ARG B 374 " --> pdb=" O   SER B 370 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 193
    Processing sheet with id=AA2, first strand: chain 'B' and resid 31 through 34
      removed outlier: 6.180A  pdb=" N   LEU B  10 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
      removed outlier: 8.057A  pdb=" N   THR B 108 " --> pdb=" O   LEU B  10 " (cutoff:3.500A)
      removed outlier: 8.108A  pdb=" N   CYS B  12 " --> pdb=" O   THR B 108 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 55 through 56
    Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 74
    Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 172
    Processing sheet with id=AA6, first strand: chain 'B' and resid 171 through 172
      removed outlier: 6.274A  pdb=" N   ASN B 299 " --> pdb=" O   ILE B 332 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 243

    317 hydrogen bonds defined for protein.
    873 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: 0.65

  Time building geometry restraints manager: 0.54 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1854
        1.34 -     1.46: 1040
        1.46 -     1.57: 2881
        1.57 -     1.69: 10
        1.69 -     1.81: 47
  Bond restraints: 5832
  Sorted by residual:
  bond pdb=" N   ILE A 316 "
       pdb=" CA  ILE A 316 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.17e-02 7.31e+03 1.03e+01
  bond pdb=" N   ILE B 359 "
       pdb=" CA  ILE B 359 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.030 1.08e-02 8.57e+03 7.65e+00
  bond pdb=" N   ASN A 164 "
       pdb=" CA  ASN A 164 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.27e-02 6.20e+03 7.00e+00
  bond pdb=" N   SER A  22 "
       pdb=" CA  SER A  22 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.20e-02 6.94e+03 4.92e+00
  bond pdb=" N   ARG A 185 "
       pdb=" CA  ARG A 185 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.33e-02 5.65e+03 4.87e+00
  ... (remaining 5827 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 7744
        1.67 -     3.33: 128
        3.33 -     5.00: 28
        5.00 -     6.67: 2
        6.67 -     8.34: 3
  Bond angle restraints: 7905
  Sorted by residual:
  angle pdb=" PB  ATP A 501 "
        pdb=" O3B ATP A 501 "
        pdb=" PG  ATP A 501 "
      ideal   model   delta    sigma   weight residual
     139.87  131.70    8.17 1.00e+00 1.00e+00 6.67e+01
  angle pdb=" PA  ATP A 501 "
        pdb=" O3A ATP A 501 "
        pdb=" PB  ATP A 501 "
      ideal   model   delta    sigma   weight residual
     136.83  132.54    4.29 1.00e+00 1.00e+00 1.84e+01
  angle pdb=" C   SER B 273 "
        pdb=" CA  SER B 273 "
        pdb=" CB  SER B 273 "
      ideal   model   delta    sigma   weight residual
     111.78  103.44    8.34 2.20e+00 2.07e-01 1.44e+01
  angle pdb=" N   THR B 360 "
        pdb=" CA  THR B 360 "
        pdb=" C   THR B 360 "
      ideal   model   delta    sigma   weight residual
     110.55  105.47    5.08 1.35e+00 5.49e-01 1.41e+01
  angle pdb=" N   ILE B 359 "
        pdb=" CA  ILE B 359 "
        pdb=" C   ILE B 359 "
      ideal   model   delta    sigma   weight residual
     108.12  103.61    4.51 1.34e+00 5.57e-01 1.13e+01
  ... (remaining 7900 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 3312
       17.66 -    35.32: 198
       35.32 -    52.98: 61
       52.98 -    70.64: 16
       70.64 -    88.30: 4
  Dihedral angle restraints: 3591
    sinusoidal: 1502
      harmonic: 2089
  Sorted by residual:
  dihedral pdb=" C   SER B 273 "
           pdb=" N   SER B 273 "
           pdb=" CA  SER B 273 "
           pdb=" CB  SER B 273 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.53   -9.07     0      2.50e+00 1.60e-01 1.32e+01
  dihedral pdb=" CA  PHE A 238 "
           pdb=" C   PHE A 238 "
           pdb=" N   VAL A 239 "
           pdb=" CA  VAL A 239 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.26   16.74     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  HIS B 163 "
           pdb=" C   HIS B 163 "
           pdb=" N   ASN B 164 "
           pdb=" CA  ASN B 164 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.36   16.64     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 3588 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 739
       0.056 -    0.112: 126
       0.112 -    0.168: 15
       0.168 -    0.224: 3
       0.224 -    0.280: 2
  Chirality restraints: 885
  Sorted by residual:
  chirality pdb=" CA  ILE B 359 "
            pdb=" N   ILE B 359 "
            pdb=" C   ILE B 359 "
            pdb=" CB  ILE B 359 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.28 2.00e-01 2.50e+01 1.97e+00
  chirality pdb=" CA  MET A 162 "
            pdb=" N   MET A 162 "
            pdb=" C   MET A 162 "
            pdb=" CB  MET A 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CA  SER B 273 "
            pdb=" N   SER B 273 "
            pdb=" C   SER B 273 "
            pdb=" CB  SER B 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 882 not shown)

  Planarity restraints: 1004
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 211 "   -0.044 5.00e-02 4.00e+02   6.73e-02 7.24e+00
        pdb=" N   PRO A 212 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 212 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 212 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 165 "   -0.021 5.00e-02 4.00e+02   3.21e-02 1.65e+00
        pdb=" N   PRO B 166 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 166 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 166 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 161 "    0.006 2.00e-02 2.50e+03   1.16e-02 1.35e+00
        pdb=" C   VAL A 161 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   VAL A 161 "    0.008 2.00e-02 2.50e+03
        pdb=" N   MET A 162 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1001 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 589
        2.74 -     3.28: 5909
        3.28 -     3.82: 10157
        3.82 -     4.36: 12580
        4.36 -     4.90: 21365
  Nonbonded interactions: 50600
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS B  90 "
            pdb=" OE2 GLU B  95 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" OE2 GLU A 343 "
            pdb=" OG  SER B 352 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OG  SER A 175 "
            pdb=" OD2 ASP A 298 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   GLY B 158 "
            pdb=" OG1 THR B 305 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OD1 ASP A  23 "
            pdb=" OG  SER A 100 "
     model   vdw
     2.243 3.040
  ... (remaining 50595 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.250
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
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      :  0.004   0.040   5832  Z= 0.213
  Angle     :  0.588   8.337   7905  Z= 0.350
  Chirality :  0.046   0.280    885
  Planarity :  0.004   0.067   1004
  Dihedral  : 13.286  88.300   2243
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.99 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  :  4.01 %
    Favored  : 92.78 %
  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 aren not related in a simple way.
  whole:  1.06 (0.32), residues: 703
  helix:  1.15 (0.27), residues: 377
  sheet: -0.26 (0.58), residues: 71
  loop :  0.54 (0.41), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 198 
 TYR   0.011   0.001   TYR A  42 
 PHE   0.012   0.001   PHE A 125 
 TRP   0.011   0.002   TRP A 277 
 HIS   0.005   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 5832)
  covalent geometry    : angle       0.58827 ( 7905)
  hydrogen bonds       : bond        0.12606 (  315)
  hydrogen bonds       : angle       5.43081 (  873)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7429 (tt)
REVERT: A  129 ASN cc_start: 0.6919 (t0) cc_final: 0.6595 (t0)
REVERT: A  162 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6515 (mtp)
REVERT: B   35 SER cc_start: 0.8187 (p) cc_final: 0.7903 (t)
REVERT: B  298 ASN cc_start: 0.7642 (m-40) cc_final: 0.7382 (m-40)
REVERT: B  336 GLU cc_start: 0.6742 (pm20) cc_final: 0.6372 (pm20)
  outliers start: 20
  outliers final: 7
  residues processed: 142
  average time/residue: 0.0741
  time to fit residues: 13.5842
Evaluate side-chains
  97 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  162 MET
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  323 GLU
Chi-restraints excluded: chain B residue   87 ILE
Chi-restraints excluded: chain B residue  143 SER
Chi-restraints excluded: chain B residue  346 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0980
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0870
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.4960

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
B 299 ASN
B 355 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.156003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.133213 restraints weight = 6390.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 1.67
r_work: 0.3486 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3347 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5832  Z= 0.134
  Angle     :  0.494   4.787   7905  Z= 0.264
  Chirality :  0.042   0.147    885
  Planarity :  0.004   0.061   1004
  Dihedral  : 10.164  84.199    856
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.14 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 10.11 %
    Favored  : 87.16 %
  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 aren not related in a simple way.
  whole:  1.41 (0.32), residues: 703
  helix:  1.35 (0.26), residues: 383
  sheet:  0.47 (0.58), residues: 71
  loop :  0.62 (0.42), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 307 
 TYR   0.036   0.001   TYR A  52 
 PHE   0.012   0.001   PHE A 125 
 TRP   0.008   0.002   TRP A 277 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5832)
  covalent geometry    : angle       0.49449 ( 7905)
  hydrogen bonds       : bond        0.03852 (  315)
  hydrogen bonds       : angle       4.38012 (  873)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 ASN cc_start: 0.7052 (t0) cc_final: 0.6654 (t0)
REVERT: B  298 ASN cc_start: 0.7417 (m-40) cc_final: 0.7206 (m-40)
REVERT: B  336 GLU cc_start: 0.6842 (pm20) cc_final: 0.6488 (pm20)
  outliers start: 17
  outliers final: 8
  residues processed: 111
  average time/residue: 0.0746
  time to fit residues: 10.8586
Evaluate side-chains
  90 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   87 ILE
Chi-restraints excluded: chain B residue  313 ASP
Chi-restraints excluded: chain B residue  331 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 57 optimal weight:    5.9990
   chunk 20 optimal weight:    0.2980
   chunk 31 optimal weight:    0.2980
   chunk 44 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN
B  75 HIS
B 355 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.156734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.133036 restraints weight = 6413.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 1.80
r_work: 0.3474 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5832  Z= 0.134
  Angle     :  0.495   6.982   7905  Z= 0.260
  Chirality :  0.043   0.180    885
  Planarity :  0.004   0.060   1004
  Dihedral  :  8.961  84.073    843
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.42 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 10.43 %
    Favored  : 87.64 %
  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 aren not related in a simple way.
  whole:  1.64 (0.32), residues: 703
  helix:  1.54 (0.26), residues: 382
  sheet:  0.76 (0.62), residues: 71
  loop :  0.65 (0.42), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 154 
 TYR   0.046   0.002   TYR A  52 
 PHE   0.013   0.001   PHE B 257 
 TRP   0.008   0.002   TRP A 277 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 5832)
  covalent geometry    : angle       0.49550 ( 7905)
  hydrogen bonds       : bond        0.03690 (  315)
  hydrogen bonds       : angle       4.20654 (  873)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
REVERT: A  129 ASN cc_start: 0.7169 (t0) cc_final: 0.6766 (t0)
REVERT: A  340 MET cc_start: 0.8164 (tmm) cc_final: 0.7913 (ttp)
REVERT: B  134 MET cc_start: 0.7661 (ttp) cc_final: 0.7263 (ttt)
REVERT: B  298 ASN cc_start: 0.7403 (m-40) cc_final: 0.7087 (m-40)
REVERT: B  315 MET cc_start: 0.7164 (tpp) cc_final: 0.6947 (tpp)
REVERT: B  336 GLU cc_start: 0.6981 (pm20) cc_final: 0.6617 (pm20)
  outliers start: 12
  outliers final: 6
  residues processed: 99
  average time/residue: 0.0600
  time to fit residues: 7.9366
Evaluate side-chains
  84 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   87 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 53 optimal weight:    0.4980
   chunk 10 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 48 optimal weight:    0.3980
   chunk 15 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.156208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.132932 restraints weight = 6459.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 1.77
r_work: 0.3480 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5832  Z= 0.135
  Angle     :  0.482   7.022   7905  Z= 0.256
  Chirality :  0.042   0.132    885
  Planarity :  0.004   0.059   1004
  Dihedral  :  8.753  84.038    843
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.85 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 11.08 %
    Favored  : 86.52 %
  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 aren not related in a simple way.
  whole:  1.73 (0.32), residues: 703
  helix:  1.61 (0.26), residues: 382
  sheet:  0.78 (0.60), residues: 71
  loop :  0.73 (0.42), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 154 
 TYR   0.044   0.001   TYR A  52 
 PHE   0.016   0.001   PHE A  24 
 TRP   0.008   0.002   TRP A 277 
 HIS   0.003   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 5832)
  covalent geometry    : angle       0.48157 ( 7905)
  hydrogen bonds       : bond        0.03576 (  315)
  hydrogen bonds       : angle       4.12819 (  873)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7458 (tp30) cc_final: 0.6890 (mt-10)
REVERT: A  129 ASN cc_start: 0.7161 (t0) cc_final: 0.6768 (t0)
REVERT: A  134 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7448 (mt-10)
REVERT: A  186 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6490 (mt-10)
REVERT: A  295 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.6937 (mp)
REVERT: A  340 MET cc_start: 0.8172 (tmm) cc_final: 0.7895 (ttp)
REVERT: B  243 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6724 (mm-30)
REVERT: B  298 ASN cc_start: 0.7483 (m-40) cc_final: 0.7135 (m-40)
REVERT: B  336 GLU cc_start: 0.7049 (pm20) cc_final: 0.6700 (pm20)
  outliers start: 15
  outliers final: 8
  residues processed: 98
  average time/residue: 0.0798
  time to fit residues: 10.2976
Evaluate side-chains
  91 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  323 GLU
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  209 GLU
Chi-restraints excluded: chain B residue  243 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 20 optimal weight:    0.2980
   chunk 8 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0000
   chunk 10 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 48 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.5784

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.156406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.133909 restraints weight = 6573.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 1.73
r_work: 0.3491 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5832  Z= 0.125
  Angle     :  0.473   7.126   7905  Z= 0.251
  Chirality :  0.042   0.126    885
  Planarity :  0.004   0.059   1004
  Dihedral  :  8.474  82.609    841
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.71 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 12.20 %
    Favored  : 85.55 %
  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 aren not related in a simple way.
  whole:  1.83 (0.32), residues: 703
  helix:  1.68 (0.26), residues: 382
  sheet:  0.84 (0.59), residues: 71
  loop :  0.79 (0.42), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 117 
 TYR   0.038   0.001   TYR A  52 
 PHE   0.019   0.001   PHE A  24 
 TRP   0.008   0.002   TRP A 277 
 HIS   0.003   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 5832)
  covalent geometry    : angle       0.47295 ( 7905)
  hydrogen bonds       : bond        0.03454 (  315)
  hydrogen bonds       : angle       4.05240 (  873)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7389 (tp30) cc_final: 0.6831 (mt-10)
REVERT: A  129 ASN cc_start: 0.7142 (t0) cc_final: 0.6737 (t0)
REVERT: A  186 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6579 (mt-10)
REVERT: A  295 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.6937 (mp)
REVERT: A  307 ARG cc_start: 0.8319 (ptp-110) cc_final: 0.8054 (mtm110)
REVERT: B  108 THR cc_start: 0.7478 (p) cc_final: 0.7225 (p)
REVERT: B  134 MET cc_start: 0.7445 (ttp) cc_final: 0.7028 (ttt)
REVERT: B  243 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6691 (mm-30)
REVERT: B  336 GLU cc_start: 0.7024 (pm20) cc_final: 0.6690 (pm20)
  outliers start: 14
  outliers final: 9
  residues processed: 102
  average time/residue: 0.0758
  time to fit residues: 10.1131
Evaluate side-chains
  94 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  323 GLU
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   87 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  178 MET
Chi-restraints excluded: chain B residue  209 GLU
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  259 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0050
   chunk 43 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0870
   chunk 64 optimal weight:    0.0170
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.5212

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.157827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.134685 restraints weight = 6412.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 1.76
r_work: 0.3497 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3355 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5832  Z= 0.121
  Angle     :  0.467   6.006   7905  Z= 0.248
  Chirality :  0.041   0.125    885
  Planarity :  0.004   0.060   1004
  Dihedral  :  8.268  81.416    841
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.56 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 12.68 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.32), residues: 703
  helix:  1.73 (0.26), residues: 382
  sheet:  0.90 (0.61), residues: 69
  loop :  0.80 (0.42), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 154 
 TYR   0.025   0.001   TYR A  52 
 PHE   0.017   0.001   PHE A  24 
 TRP   0.008   0.001   TRP A 277 
 HIS   0.003   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 5832)
  covalent geometry    : angle       0.46650 ( 7905)
  hydrogen bonds       : bond        0.03380 (  315)
  hydrogen bonds       : angle       3.98781 (  873)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7415 (tp30) cc_final: 0.6844 (mt-10)
REVERT: A  129 ASN cc_start: 0.7139 (t0) cc_final: 0.6743 (t0)
REVERT: A  186 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6627 (mt-10)
REVERT: A  295 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.6964 (mp)
REVERT: A  307 ARG cc_start: 0.8278 (ptp-110) cc_final: 0.7896 (mtp180)
REVERT: B  108 THR cc_start: 0.7452 (p) cc_final: 0.7199 (p)
REVERT: B  134 MET cc_start: 0.7429 (ttp) cc_final: 0.7014 (ttt)
REVERT: B  243 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6721 (mm-30)
REVERT: B  336 GLU cc_start: 0.7035 (pm20) cc_final: 0.6680 (pm20)
  outliers start: 17
  outliers final: 10
  residues processed: 101
  average time/residue: 0.0749
  time to fit residues: 10.0323
Evaluate side-chains
  94 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  323 GLU
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   87 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  178 MET
Chi-restraints excluded: chain B residue  209 GLU
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  259 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 18 optimal weight:    0.4980
   chunk 60 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 29 optimal weight:    0.2980
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3864 r_free = 0.3864 target = 0.156411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.132873 restraints weight = 6566.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 1.80
r_work: 0.3476 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3335 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5832  Z= 0.131
  Angle     :  0.475   5.676   7905  Z= 0.253
  Chirality :  0.042   0.128    885
  Planarity :  0.004   0.059   1004
  Dihedral  :  8.226  81.441    841
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.71 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.00 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.90 (0.32), residues: 703
  helix:  1.73 (0.26), residues: 382
  sheet:  0.94 (0.62), residues: 69
  loop :  0.80 (0.42), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 154 
 TYR   0.019   0.001   TYR A  52 
 PHE   0.021   0.002   PHE A  24 
 TRP   0.008   0.002   TRP A 277 
 HIS   0.003   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 5832)
  covalent geometry    : angle       0.47490 ( 7905)
  hydrogen bonds       : bond        0.03453 (  315)
  hydrogen bonds       : angle       3.97355 (  873)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7478 (tp30) cc_final: 0.6944 (mt-10)
REVERT: A   52 TYR cc_start: 0.7418 (m-80) cc_final: 0.7170 (m-80)
REVERT: A  129 ASN cc_start: 0.7135 (t0) cc_final: 0.6730 (t0)
REVERT: A  186 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6664 (mt-10)
REVERT: A  295 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7002 (mp)
REVERT: B  108 THR cc_start: 0.7517 (p) cc_final: 0.7270 (p)
REVERT: B  134 MET cc_start: 0.7419 (ttp) cc_final: 0.6983 (ttt)
REVERT: B  243 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6729 (mm-30)
REVERT: B  336 GLU cc_start: 0.7072 (pm20) cc_final: 0.6716 (pm20)
  outliers start: 13
  outliers final: 9
  residues processed: 97
  average time/residue: 0.0716
  time to fit residues: 9.4531
Evaluate side-chains
  93 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   89 SER
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   87 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  178 MET
Chi-restraints excluded: chain B residue  209 GLU
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  259 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0170
   chunk 62 optimal weight:    0.9980
   chunk 50 optimal weight:    0.3980
   chunk 19 optimal weight:    0.0040
   chunk 17 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0270
   chunk 27 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.2888

-------------------------------------------------------------------------------
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 = 0.3905 r_free = 0.3905 target = 0.158322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.136800 restraints weight = 6468.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 1.58
r_work: 0.3549 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3414 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.2558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   5832  Z= 0.104
  Angle     :  0.460   7.410   7905  Z= 0.244
  Chirality :  0.041   0.125    885
  Planarity :  0.004   0.059   1004
  Dihedral  :  7.989  79.479    841
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.29 %
    Favored  : 84.27 %
  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 aren not related in a simple way.
  whole:  2.11 (0.32), residues: 703
  helix:  1.90 (0.26), residues: 382
  sheet:  1.08 (0.63), residues: 69
  loop :  0.89 (0.42), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 154 
 TYR   0.012   0.001   TYR A  42 
 PHE   0.025   0.002   PHE A  31 
 TRP   0.008   0.001   TRP A 277 
 HIS   0.003   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 5832)
  covalent geometry    : angle       0.46002 ( 7905)
  hydrogen bonds       : bond        0.03196 (  315)
  hydrogen bonds       : angle       3.87807 (  873)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7355 (tp30) cc_final: 0.6778 (mt-10)
REVERT: A   52 TYR cc_start: 0.7317 (m-80) cc_final: 0.7103 (m-80)
REVERT: A  129 ASN cc_start: 0.7085 (t0) cc_final: 0.6652 (t0)
REVERT: A  186 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6688 (mt-10)
REVERT: A  295 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.6967 (mp)
REVERT: B  243 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6645 (mm-30)
REVERT: B  336 GLU cc_start: 0.6772 (pm20) cc_final: 0.6463 (pm20)
  outliers start: 9
  outliers final: 6
  residues processed: 97
  average time/residue: 0.0707
  time to fit residues: 9.1381
Evaluate side-chains
  95 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   87 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  209 GLU
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  259 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0370
   chunk 59 optimal weight:    0.0020
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.4866

-------------------------------------------------------------------------------
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 = 0.3887 r_free = 0.3887 target = 0.156506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.135450 restraints weight = 6457.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 1.52
r_work: 0.3518 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5832  Z= 0.117
  Angle     :  0.470   7.602   7905  Z= 0.249
  Chirality :  0.041   0.127    885
  Planarity :  0.004   0.059   1004
  Dihedral  :  7.897  80.240    839
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.29 %
    Favored  : 84.11 %
  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 aren not related in a simple way.
  whole:  2.09 (0.32), residues: 703
  helix:  1.88 (0.26), residues: 382
  sheet:  1.01 (0.63), residues: 69
  loop :  0.91 (0.42), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 154 
 TYR   0.013   0.001   TYR A  42 
 PHE   0.034   0.002   PHE A  31 
 TRP   0.007   0.001   TRP A 277 
 HIS   0.003   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 5832)
  covalent geometry    : angle       0.47016 ( 7905)
  hydrogen bonds       : bond        0.03317 (  315)
  hydrogen bonds       : angle       3.89198 (  873)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7312 (tp30) cc_final: 0.6767 (mt-10)
REVERT: A  129 ASN cc_start: 0.7050 (t0) cc_final: 0.6652 (t0)
REVERT: A  186 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6073 (mp0)
REVERT: A  295 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.6971 (mp)
REVERT: B  108 THR cc_start: 0.7481 (p) cc_final: 0.7202 (p)
REVERT: B  243 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6566 (mm-30)
REVERT: B  336 GLU cc_start: 0.6782 (pm20) cc_final: 0.6473 (pm20)
  outliers start: 10
  outliers final: 6
  residues processed: 95
  average time/residue: 0.0633
  time to fit residues: 8.2058
Evaluate side-chains
  96 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   87 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  259 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 16 optimal weight:    0.2980
   chunk 66 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0980
   chunk 68 optimal weight:    0.0970
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.3778

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

Flipped N/Q/H residues before XYZ refinement:
** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.159045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.136625 restraints weight = 6529.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 1.70
r_work: 0.3529 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3392 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5832  Z= 0.111
  Angle     :  0.471   4.759   7905  Z= 0.254
  Chirality :  0.042   0.128    885
  Planarity :  0.004   0.059   1004
  Dihedral  :  7.823  79.941    839
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.77 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.32), residues: 703
  helix:  1.86 (0.26), residues: 382
  sheet:  1.13 (0.64), residues: 69
  loop :  0.92 (0.42), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 154 
 TYR   0.015   0.001   TYR A  52 
 PHE   0.038   0.002   PHE A  31 
 TRP   0.008   0.001   TRP A 277 
 HIS   0.003   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 5832)
  covalent geometry    : angle       0.47114 ( 7905)
  hydrogen bonds       : bond        0.03326 (  315)
  hydrogen bonds       : angle       3.93438 (  873)

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

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

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1406 Ramachandran restraints generated.
    703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7341 (tp30) cc_final: 0.6722 (mt-10)
REVERT: A   52 TYR cc_start: 0.7385 (m-80) cc_final: 0.6942 (m-80)
REVERT: A  129 ASN cc_start: 0.7126 (t0) cc_final: 0.6722 (t0)
REVERT: A  186 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6058 (mp0)
REVERT: A  295 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.6911 (mp)
REVERT: B  108 THR cc_start: 0.7408 (p) cc_final: 0.7132 (p)
REVERT: B  243 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6598 (mm-30)
REVERT: B  336 GLU cc_start: 0.6868 (pm20) cc_final: 0.6514 (pm20)
  outliers start: 9
  outliers final: 6
  residues processed: 99
  average time/residue: 0.0610
  time to fit residues: 8.2975
Evaluate side-chains
  98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   87 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  209 GLU
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  259 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0870
   chunk 43 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0000
   overall best weight:    0.3762

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN
** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.159143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.136899 restraints weight = 6382.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 1.68
r_work: 0.3536 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3398 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.2749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5832  Z= 0.111
  Angle     :  0.476   4.766   7905  Z= 0.256
  Chirality :  0.042   0.134    885
  Planarity :  0.004   0.059   1004
  Dihedral  :  7.776  79.790    839
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 14.61 %
    Favored  : 83.63 %
  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 aren not related in a simple way.
  whole:  2.13 (0.32), residues: 703
  helix:  1.88 (0.26), residues: 382
  sheet:  1.15 (0.64), residues: 69
  loop :  0.94 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 154 
 TYR   0.022   0.001   TYR A  52 
 PHE   0.034   0.002   PHE A  31 
 TRP   0.008   0.001   TRP A 277 
 HIS   0.003   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 5832)
  covalent geometry    : angle       0.47597 ( 7905)
  hydrogen bonds       : bond        0.03277 (  315)
  hydrogen bonds       : angle       3.94309 (  873)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1487.73 seconds
wall clock time: 26 minutes 11.20 seconds (1571.20 seconds total)