Starting phenix.real_space_refine
on Wed Jul 23 10:10:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cog_16776/07_2025/8cog_16776.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cog_16776/07_2025/8cog_16776.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.499
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cog_16776/07_2025/8cog_16776.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cog_16776/07_2025/8cog_16776.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cog_16776/07_2025/8cog_16776.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cog_16776/07_2025/8cog_16776.cif"
  }
  resolution = 3.499
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      1      5.21       5
     S      22      5.16       5
     C    1858      2.51       5
     N     498      2.21       5
     O     568      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 2949
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "F"
      Number of atoms: 2921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 374, 2921
          Classifications: {'peptide': 374}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 354}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.67, per 1000 atoms: 0.91
  Number of scatterers: 2949
  At special positions: 0
  Unit cell: (79.92, 62.64, 82.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      22     16.00
     P       2     15.00
     Mg      1     11.99
     O     568      8.00
     N     498      7.00
     C    1858      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS F 216 " - pdb=" SG  CYS F 256 " distance=2.10

  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: 0.80
  Conformation dependent library (CDL) restraints added in 339.2 milliseconds
  

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  692

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 6 sheets defined
      45.7% alpha, 15.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'F' and resid 54 through 60
      removed outlier: 4.060A  pdb=" N   GLN F  58 " --> pdb=" O   GLY F  54 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 77 through 91
    Processing helix  chain 'F' and resid 111 through 125
      removed outlier: 4.157A  pdb=" N   ARG F 115 " --> pdb=" O   PRO F 111 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 136 through 145
    Processing helix  chain 'F' and resid 171 through 174
    Processing helix  chain 'F' and resid 180 through 193
      removed outlier: 3.554A  pdb=" N   LYS F 190 " --> pdb=" O   ASP F 186 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   THR F 193 " --> pdb=" O   MET F 189 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 201 through 216
    Processing helix  chain 'F' and resid 221 through 232
    Processing helix  chain 'F' and resid 250 through 255
    Processing helix  chain 'F' and resid 256 through 262
      removed outlier: 4.021A  pdb=" N   ALA F 259 " --> pdb=" O   CYS F 256 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 272 through 282
    Processing helix  chain 'F' and resid 285 through 294
      removed outlier: 4.201A  pdb=" N   LYS F 290 " --> pdb=" O   VAL F 286 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   ASP F 291 " --> pdb=" O   ASP F 287 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 307 through 320
      removed outlier: 3.582A  pdb=" N   LYS F 314 " --> pdb=" O   ASP F 310 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 333 through 335
      No H-bonds generated for 'chain 'F' and resid 333 through 335'
    Processing helix  chain 'F' and resid 336 through 348
    Processing helix  chain 'F' and resid 358 through 365
      removed outlier: 3.802A  pdb=" N   GLU F 363 " --> pdb=" O   GLN F 359 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 368 through 373
    Processing sheet with id=AA1, first strand: chain 'F' and resid 16 through 17
      removed outlier: 4.125A  pdb=" N   LYS F  17 " --> pdb=" O   ASP F  10 " (cutoff:3.500A)
      removed outlier: 5.010A  pdb=" N   ASN F  11 " --> pdb=" O   THR F 105 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 52 through 53
      removed outlier: 3.518A  pdb=" N   GLY F  35 " --> pdb=" O   TYR F  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 70 through 71
    Processing sheet with id=AA4, first strand: chain 'F' and resid 168 through 169
    Processing sheet with id=AA5, first strand: chain 'F' and resid 168 through 169
    Processing sheet with id=AA6, first strand: chain 'F' and resid 237 through 240

    140 hydrogen bonds defined for protein.
    366 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: 0.83

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        0.86 -     1.06: 1
        1.06 -     1.25: 329
        1.25 -     1.45: 949
        1.45 -     1.64: 1696
        1.64 -     1.84: 38
  Bond restraints: 3013
  Sorted by residual:
  bond pdb=" C   PHE F 374 "
       pdb=" O   PHE F 374 "
    ideal  model  delta    sigma   weight residual
    1.231  0.861  0.370 2.00e-02 2.50e+03 3.43e+02
  bond pdb=" C   PHE F 374 "
       pdb=" OXT PHE F 374 "
    ideal  model  delta    sigma   weight residual
    1.231  1.547 -0.316 2.00e-02 2.50e+03 2.50e+02
  bond pdb=" C4  ADP F 401 "
       pdb=" C5  ADP F 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.392  0.098 2.00e-02 2.50e+03 2.38e+01
  bond pdb=" N   ALA F 330 "
       pdb=" CA  ALA F 330 "
    ideal  model  delta    sigma   weight residual
    1.460  1.492 -0.032 7.10e-03 1.98e+04 1.99e+01
  bond pdb=" N   VAL F 162 "
       pdb=" CA  VAL F 162 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.037 8.70e-03 1.32e+04 1.80e+01
  ... (remaining 3008 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.44: 3978
        4.44 -     8.88: 99
        8.88 -    13.32: 9
       13.32 -    17.76: 0
       17.76 -    22.20: 1
  Bond angle restraints: 4087
  Sorted by residual:
  angle pdb=" CA  PHE F 374 "
        pdb=" C   PHE F 374 "
        pdb=" OXT PHE F 374 "
      ideal   model   delta    sigma   weight residual
     121.00   98.80   22.20 3.00e+00 1.11e-01 5.48e+01
  angle pdb=" C   PRO F 242 "
        pdb=" N   ASP F 243 "
        pdb=" CA  ASP F 243 "
      ideal   model   delta    sigma   weight residual
     120.28  128.35   -8.07 1.44e+00 4.82e-01 3.14e+01
  angle pdb=" CA  PHE F 261 "
        pdb=" C   PHE F 261 "
        pdb=" O   PHE F 261 "
      ideal   model   delta    sigma   weight residual
     119.38  112.89    6.49 1.23e+00 6.61e-01 2.78e+01
  angle pdb=" N   HIS F 274 "
        pdb=" CA  HIS F 274 "
        pdb=" C   HIS F 274 "
      ideal   model   delta    sigma   weight residual
     111.69  105.95    5.74 1.23e+00 6.61e-01 2.18e+01
  angle pdb=" N   LYS F 283 "
        pdb=" CA  LYS F 283 "
        pdb=" C   LYS F 283 "
      ideal   model   delta    sigma   weight residual
     113.23  107.48    5.75 1.24e+00 6.50e-01 2.15e+01
  ... (remaining 4082 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.00: 1686
       25.00 -    50.01: 98
       50.01 -    75.01: 28
       75.01 -   100.02: 4
      100.02 -   125.02: 1
  Dihedral angle restraints: 1817
    sinusoidal: 737
      harmonic: 1080
  Sorted by residual:
  dihedral pdb=" O1B ADP F 401 "
           pdb=" O3A ADP F 401 "
           pdb=" PB  ADP F 401 "
           pdb=" PA  ADP F 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  174.97  125.02     1      2.00e+01 2.50e-03 3.78e+01
  dihedral pdb=" CA  ARG F  27 "
           pdb=" C   ARG F  27 "
           pdb=" N   ALA F  28 "
           pdb=" CA  ALA F  28 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.60  -25.40     0      5.00e+00 4.00e-02 2.58e+01
  dihedral pdb=" CA  ARG F 195 "
           pdb=" C   ARG F 195 "
           pdb=" N   GLY F 196 "
           pdb=" CA  GLY F 196 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.87   22.13     0      5.00e+00 4.00e-02 1.96e+01
  ... (remaining 1814 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.056: 188
       0.056 -    0.112: 153
       0.112 -    0.168: 81
       0.168 -    0.223: 24
       0.223 -    0.279: 7
  Chirality restraints: 453
  Sorted by residual:
  chirality pdb=" CA  VAL F   9 "
            pdb=" N   VAL F   9 "
            pdb=" C   VAL F   9 "
            pdb=" CB  VAL F   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.72   -0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" CA  ILE F 249 "
            pdb=" N   ILE F 249 "
            pdb=" C   ILE F 249 "
            pdb=" CB  ILE F 249 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" CA  VAL F   8 "
            pdb=" N   VAL F   8 "
            pdb=" C   VAL F   8 "
            pdb=" CB  VAL F   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.26 2.00e-01 2.50e+01 1.64e+00
  ... (remaining 450 not shown)

  Planarity restraints: 523
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' ADP F 401 "    0.092 2.00e-02 2.50e+03   3.97e-02 4.33e+01
        pdb=" C2  ADP F 401 "   -0.039 2.00e-02 2.50e+03
        pdb=" C4  ADP F 401 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5  ADP F 401 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6  ADP F 401 "    0.008 2.00e-02 2.50e+03
        pdb=" C8  ADP F 401 "   -0.042 2.00e-02 2.50e+03
        pdb=" N1  ADP F 401 "    0.004 2.00e-02 2.50e+03
        pdb=" N3  ADP F 401 "   -0.007 2.00e-02 2.50e+03
        pdb=" N6  ADP F 401 "    0.057 2.00e-02 2.50e+03
        pdb=" N7  ADP F 401 "   -0.022 2.00e-02 2.50e+03
        pdb=" N9  ADP F 401 "   -0.040 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE F 374 "    0.021 2.00e-02 2.50e+03   5.21e-02 2.72e+01
        pdb=" C   PHE F 374 "   -0.088 2.00e-02 2.50e+03
        pdb=" O   PHE F 374 "    0.048 2.00e-02 2.50e+03
        pdb=" OXT PHE F 374 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE F  30 "   -0.041 2.00e-02 2.50e+03   2.77e-02 1.35e+01
        pdb=" CG  PHE F  30 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE F  30 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 PHE F  30 "    0.018 2.00e-02 2.50e+03
        pdb=" CE1 PHE F  30 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 PHE F  30 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE F  30 "   -0.042 2.00e-02 2.50e+03
  ... (remaining 520 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 799
        2.86 -     3.37: 3094
        3.37 -     3.88: 4750
        3.88 -     4.39: 5826
        4.39 -     4.90: 9265
  Nonbonded interactions: 23734
  Sorted by model distance:
  nonbonded pdb=" O   ILE F 121 "
            pdb=" OG1 THR F 125 "
     model   vdw
     2.346 3.040
  nonbonded pdb=" OG  SER F  13 "
            pdb=" O   ASP F 156 "
     model   vdw
     2.417 3.040
  nonbonded pdb=" O2B ADP F 401 "
            pdb="MG    MG F 402 "
     model   vdw
     2.435 2.170
  nonbonded pdb=" OG1 THR F 148 "
            pdb=" N   GLU F 166 "
     model   vdw
     2.438 3.120
  nonbonded pdb=" O2' ADP F 401 "
            pdb=" O3' ADP F 401 "
     model   vdw
     2.443 2.432
  ... (remaining 23729 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=0.00 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:             1.430
  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:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.900
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.017   0.370   3014  Z= 1.141
  Angle     :  2.048  22.203   4089  Z= 1.412
  Chirality :  0.094   0.279    453
  Planarity :  0.008   0.052    523
  Dihedral  : 17.629 125.023   1122
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 11.71 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.96 (0.39), residues: 369
  helix: -2.12 (0.36), residues: 144
  sheet: -0.10 (0.83), residues: 35
  loop : -2.20 (0.43), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.012   TRP F  78 
 HIS   0.010   0.004   HIS F  86 
 PHE   0.042   0.010   PHE F  30 
 TYR   0.041   0.009   TYR F  68 
 ARG   0.025   0.003   ARG F 311 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27929 (  138)
  hydrogen bonds       : angle       9.74922 (  366)
  SS BOND              : bond        0.06635 (    1)
  SS BOND              : angle       5.79690 (    2)
  covalent geometry    : bond        0.01700 ( 3013)
  covalent geometry    : angle       2.04416 ( 4087)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: F    4 ILE cc_start: 0.8449 (pt) cc_final: 0.8141 (mt)
REVERT: F   11 ASN cc_start: 0.9091 (t0) cc_final: 0.8707 (p0)
REVERT: F   40 GLN cc_start: 0.7500 (mt0) cc_final: 0.7162 (pm20)
REVERT: F  182 ARG cc_start: 0.8514 (ttp80) cc_final: 0.8285 (tpp80)
REVERT: F  240 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7352 (pp20)
REVERT: F  313 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7474 (tp40)
  outliers start: 7
  outliers final: 0
  residues processed: 89
  average time/residue: 0.1878
  time to fit residues: 19.4482
Evaluate side-chains
  54 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 136 GLN
** F 352 GLN ** 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 = 0.3502 r_free = 0.3502 target = 0.131380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.116005 restraints weight = 4105.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 1.80
r_work: 0.3221 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.2804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3014  Z= 0.162
  Angle     :  0.714   7.419   4089  Z= 0.365
  Chirality :  0.048   0.293    453
  Planarity :  0.005   0.037    523
  Dihedral  :  8.470 112.926    420
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 17.09 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.42), residues: 369
  helix: -0.35 (0.39), residues: 155
  sheet: -1.04 (0.64), residues: 65
  loop : -1.50 (0.48), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP F  85 
 HIS   0.005   0.001   HIS F 370 
 PHE   0.013   0.002   PHE F 261 
 TYR   0.017   0.002   TYR F 293 
 ARG   0.003   0.001   ARG F 195 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05253 (  138)
  hydrogen bonds       : angle       5.38139 (  366)
  SS BOND              : bond        0.00029 (    1)
  SS BOND              : angle       1.30399 (    2)
  covalent geometry    : bond        0.00371 ( 3013)
  covalent geometry    : angle       0.71347 ( 4087)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.345 
Fit side-chains
REVERT: F    4 ILE cc_start: 0.8161 (pt) cc_final: 0.7835 (mt)
REVERT: F  136 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8324 (mm-40)
REVERT: F  142 TYR cc_start: 0.8625 (m-80) cc_final: 0.8422 (m-80)
REVERT: F  324 MET cc_start: 0.4339 (OUTLIER) cc_final: 0.4004 (tpp)
  outliers start: 8
  outliers final: 5
  residues processed: 65
  average time/residue: 0.1119
  time to fit residues: 9.3480
Evaluate side-chains
  55 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   33 ILE
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue  136 GLN
Chi-restraints excluded: chain F residue  238 SER
Chi-restraints excluded: chain F residue  256 CYS
Chi-restraints excluded: chain F residue  324 MET
Chi-restraints excluded: chain F residue  348 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 19 optimal weight:    0.4980
   chunk 17 optimal weight:    0.0980
   chunk 11 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 0 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3517 r_free = 0.3517 target = 0.132172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.116684 restraints weight = 4049.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 1.75
r_work: 0.3213 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3014  Z= 0.130
  Angle     :  0.654   8.560   4089  Z= 0.324
  Chirality :  0.045   0.147    453
  Planarity :  0.004   0.038    523
  Dihedral  :  7.742  98.718    420
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 18.04 %
    Favored  : 78.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.43), residues: 369
  helix:  0.18 (0.41), residues: 156
  sheet: -0.28 (0.64), residues: 65
  loop : -1.37 (0.49), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP F  78 
 HIS   0.005   0.001   HIS F 370 
 PHE   0.013   0.001   PHE F 254 
 TYR   0.011   0.001   TYR F 293 
 ARG   0.003   0.000   ARG F 195 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03863 (  138)
  hydrogen bonds       : angle       4.76551 (  366)
  SS BOND              : bond        0.00122 (    1)
  SS BOND              : angle       1.05218 (    2)
  covalent geometry    : bond        0.00297 ( 3013)
  covalent geometry    : angle       0.65368 ( 4087)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.316 
Fit side-chains
REVERT: F  313 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7326 (tp40)
REVERT: F  324 MET cc_start: 0.3991 (OUTLIER) cc_final: 0.3659 (tpp)
  outliers start: 11
  outliers final: 7
  residues processed: 60
  average time/residue: 0.1041
  time to fit residues: 8.1648
Evaluate side-chains
  51 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   13 SER
Chi-restraints excluded: chain F residue   33 ILE
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   70 ILE
Chi-restraints excluded: chain F residue  148 THR
Chi-restraints excluded: chain F residue  238 SER
Chi-restraints excluded: chain F residue  256 CYS
Chi-restraints excluded: chain F residue  324 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 23 optimal weight:    0.0870
   chunk 25 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0970
   chunk 32 optimal weight:    0.0040
   chunk 27 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0000
   overall best weight:    0.1772

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

Flipped N/Q/H residues before XYZ refinement:
F 100 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.135772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.120582 restraints weight = 4100.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 1.74
r_work: 0.3284 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.3981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   3014  Z= 0.107
  Angle     :  0.594   6.949   4089  Z= 0.295
  Chirality :  0.043   0.159    453
  Planarity :  0.004   0.034    523
  Dihedral  :  7.337  89.757    420
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 18.35 %
    Favored  : 78.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.44), residues: 369
  helix:  0.88 (0.44), residues: 150
  sheet:  0.28 (0.61), residues: 65
  loop : -1.34 (0.49), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F  78 
 HIS   0.003   0.001   HIS F 370 
 PHE   0.013   0.001   PHE F 254 
 TYR   0.011   0.001   TYR F 293 
 ARG   0.002   0.000   ARG F 195 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03081 (  138)
  hydrogen bonds       : angle       4.40731 (  366)
  SS BOND              : bond        0.00038 (    1)
  SS BOND              : angle       0.61834 (    2)
  covalent geometry    : bond        0.00236 ( 3013)
  covalent geometry    : angle       0.59372 ( 4087)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.345 
Fit side-chains
REVERT: F  282 MET cc_start: 0.8343 (mmm) cc_final: 0.8132 (mmm)
  outliers start: 10
  outliers final: 5
  residues processed: 64
  average time/residue: 0.1195
  time to fit residues: 9.7586
Evaluate side-chains
  46 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   13 SER
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   70 ILE
Chi-restraints excluded: chain F residue  148 THR
Chi-restraints excluded: chain F residue  256 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 30 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 36 optimal weight:    4.9990
   chunk 4 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
F  77 ASN
F 136 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.130621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.115466 restraints weight = 4186.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3318 rms_B_bonded: 1.74
r_work: 0.3231 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.4283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3014  Z= 0.131
  Angle     :  0.626   7.209   4089  Z= 0.305
  Chirality :  0.044   0.148    453
  Planarity :  0.004   0.032    523
  Dihedral  :  7.294  88.758    420
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 19.30 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.43), residues: 369
  helix:  0.85 (0.43), residues: 150
  sheet:  0.48 (0.64), residues: 65
  loop : -1.22 (0.48), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F  78 
 HIS   0.003   0.001   HIS F 100 
 PHE   0.014   0.001   PHE F 254 
 TYR   0.018   0.001   TYR F  52 
 ARG   0.003   0.000   ARG F 195 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03337 (  138)
  hydrogen bonds       : angle       4.31332 (  366)
  SS BOND              : bond        0.00165 (    1)
  SS BOND              : angle       1.14716 (    2)
  covalent geometry    : bond        0.00308 ( 3013)
  covalent geometry    : angle       0.62545 ( 4087)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.355 
Fit side-chains
REVERT: F  282 MET cc_start: 0.8393 (mmm) cc_final: 0.8165 (mmm)
REVERT: F  324 MET cc_start: 0.3982 (OUTLIER) cc_final: 0.3598 (tpp)
REVERT: F  345 LEU cc_start: 0.9006 (tp) cc_final: 0.8761 (tt)
  outliers start: 12
  outliers final: 8
  residues processed: 57
  average time/residue: 0.1366
  time to fit residues: 9.9202
Evaluate side-chains
  54 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   13 SER
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   70 ILE
Chi-restraints excluded: chain F residue   77 ASN
Chi-restraints excluded: chain F residue  122 MET
Chi-restraints excluded: chain F residue  148 THR
Chi-restraints excluded: chain F residue  238 SER
Chi-restraints excluded: chain F residue  256 CYS
Chi-restraints excluded: chain F residue  324 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 10 optimal weight:    0.1980
   chunk 32 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
F  77 ASN
** F 136 GLN ** 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 = 0.3461 r_free = 0.3461 target = 0.127513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.113043 restraints weight = 4315.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 1.81
r_work: 0.3185 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.4320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3014  Z= 0.127
  Angle     :  0.611   6.966   4089  Z= 0.298
  Chirality :  0.044   0.144    453
  Planarity :  0.004   0.033    523
  Dihedral  :  7.292  88.867    420
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 20.25 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.44), residues: 369
  helix:  1.09 (0.44), residues: 143
  sheet:  0.46 (0.64), residues: 65
  loop : -1.01 (0.48), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F  78 
 HIS   0.003   0.001   HIS F 100 
 PHE   0.013   0.001   PHE F 254 
 TYR   0.013   0.001   TYR F  52 
 ARG   0.003   0.000   ARG F 195 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03208 (  138)
  hydrogen bonds       : angle       4.30467 (  366)
  SS BOND              : bond        0.00107 (    1)
  SS BOND              : angle       1.03658 (    2)
  covalent geometry    : bond        0.00298 ( 3013)
  covalent geometry    : angle       0.61027 ( 4087)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.318 
Fit side-chains
REVERT: F  282 MET cc_start: 0.8398 (mmm) cc_final: 0.8162 (mmm)
REVERT: F  345 LEU cc_start: 0.8997 (tp) cc_final: 0.8768 (tt)
  outliers start: 10
  outliers final: 6
  residues processed: 53
  average time/residue: 0.1195
  time to fit residues: 8.0895
Evaluate side-chains
  50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   13 SER
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   70 ILE
Chi-restraints excluded: chain F residue  148 THR
Chi-restraints excluded: chain F residue  238 SER
Chi-restraints excluded: chain F residue  256 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
F  77 ASN
** F 136 GLN ** 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 = 0.3423 r_free = 0.3423 target = 0.124226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.109992 restraints weight = 4344.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 1.79
r_work: 0.3150 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3031 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.4382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3014  Z= 0.169
  Angle     :  0.637   6.957   4089  Z= 0.315
  Chirality :  0.046   0.152    453
  Planarity :  0.004   0.038    523
  Dihedral  :  7.596  95.132    420
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 19.62 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.43), residues: 369
  helix:  0.92 (0.44), residues: 143
  sheet:  0.73 (0.65), residues: 60
  loop : -1.08 (0.47), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP F  78 
 HIS   0.004   0.001   HIS F 100 
 PHE   0.014   0.002   PHE F 254 
 TYR   0.012   0.001   TYR F 293 
 ARG   0.003   0.000   ARG F 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03790 (  138)
  hydrogen bonds       : angle       4.34523 (  366)
  SS BOND              : bond        0.00262 (    1)
  SS BOND              : angle       1.51302 (    2)
  covalent geometry    : bond        0.00410 ( 3013)
  covalent geometry    : angle       0.63584 ( 4087)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 47
  time to evaluate  : 0.353 
Fit side-chains
REVERT: F  282 MET cc_start: 0.8383 (mmm) cc_final: 0.8113 (mmm)
REVERT: F  324 MET cc_start: 0.3867 (OUTLIER) cc_final: 0.3533 (tpp)
REVERT: F  354 MET cc_start: 0.8046 (mmm) cc_final: 0.7755 (mpp)
  outliers start: 13
  outliers final: 10
  residues processed: 55
  average time/residue: 0.1134
  time to fit residues: 8.1643
Evaluate side-chains
  54 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   13 SER
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   77 ASN
Chi-restraints excluded: chain F residue  122 MET
Chi-restraints excluded: chain F residue  148 THR
Chi-restraints excluded: chain F residue  238 SER
Chi-restraints excluded: chain F residue  240 GLU
Chi-restraints excluded: chain F residue  256 CYS
Chi-restraints excluded: chain F residue  303 THR
Chi-restraints excluded: chain F residue  324 MET
Chi-restraints excluded: chain F residue  369 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 36 optimal weight:    0.4980
   chunk 27 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 30 optimal weight:    0.4980
   chunk 16 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** F 136 GLN ** 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 = 0.3447 r_free = 0.3447 target = 0.126451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.112919 restraints weight = 4269.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 1.66
r_work: 0.3180 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.4484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3014  Z= 0.131
  Angle     :  0.614   6.850   4089  Z= 0.303
  Chirality :  0.044   0.142    453
  Planarity :  0.004   0.036    523
  Dihedral  :  7.531  95.019    420
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 19.30 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.43), residues: 369
  helix:  1.03 (0.44), residues: 143
  sheet:  0.79 (0.64), residues: 60
  loop : -1.02 (0.47), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP F  78 
 HIS   0.003   0.001   HIS F 100 
 PHE   0.012   0.001   PHE F 254 
 TYR   0.011   0.001   TYR F 293 
 ARG   0.002   0.000   ARG F 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03312 (  138)
  hydrogen bonds       : angle       4.29515 (  366)
  SS BOND              : bond        0.00165 (    1)
  SS BOND              : angle       1.07349 (    2)
  covalent geometry    : bond        0.00313 ( 3013)
  covalent geometry    : angle       0.61384 ( 4087)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.350 
Fit side-chains
REVERT: F    7 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8369 (mt)
REVERT: F  282 MET cc_start: 0.8333 (mmm) cc_final: 0.8044 (mmm)
REVERT: F  354 MET cc_start: 0.7986 (mmm) cc_final: 0.7696 (mpp)
REVERT: F  370 HIS cc_start: 0.8521 (m-70) cc_final: 0.8319 (m90)
  outliers start: 14
  outliers final: 10
  residues processed: 53
  average time/residue: 0.1120
  time to fit residues: 7.8359
Evaluate side-chains
  56 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    7 LEU
Chi-restraints excluded: chain F residue   13 SER
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue  122 MET
Chi-restraints excluded: chain F residue  142 TYR
Chi-restraints excluded: chain F residue  148 THR
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  238 SER
Chi-restraints excluded: chain F residue  240 GLU
Chi-restraints excluded: chain F residue  256 CYS
Chi-restraints excluded: chain F residue  303 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0870
   chunk 36 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
F  77 ASN
** F 136 GLN ** 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 = 0.3465 r_free = 0.3465 target = 0.127488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.113276 restraints weight = 4230.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 1.78
r_work: 0.3200 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.4635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3014  Z= 0.119
  Angle     :  0.598   6.905   4089  Z= 0.292
  Chirality :  0.043   0.140    453
  Planarity :  0.004   0.031    523
  Dihedral  :  7.357  92.513    420
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.57 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.44), residues: 369
  helix:  1.16 (0.44), residues: 143
  sheet:  0.85 (0.64), residues: 60
  loop : -0.92 (0.48), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F  78 
 HIS   0.003   0.001   HIS F 100 
 PHE   0.013   0.001   PHE F 254 
 TYR   0.010   0.001   TYR F  52 
 ARG   0.001   0.000   ARG F 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02935 (  138)
  hydrogen bonds       : angle       4.18200 (  366)
  SS BOND              : bond        0.00122 (    1)
  SS BOND              : angle       0.88785 (    2)
  covalent geometry    : bond        0.00282 ( 3013)
  covalent geometry    : angle       0.59785 ( 4087)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.369 
Fit side-chains
REVERT: F    7 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8339 (mt)
REVERT: F  282 MET cc_start: 0.8243 (mmm) cc_final: 0.7995 (mmm)
REVERT: F  324 MET cc_start: 0.3840 (OUTLIER) cc_final: 0.3622 (tpp)
REVERT: F  354 MET cc_start: 0.7892 (mmm) cc_final: 0.7621 (mpp)
REVERT: F  370 HIS cc_start: 0.8483 (m-70) cc_final: 0.8249 (m90)
  outliers start: 12
  outliers final: 9
  residues processed: 55
  average time/residue: 0.1251
  time to fit residues: 8.9350
Evaluate side-chains
  55 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue    7 LEU
Chi-restraints excluded: chain F residue   13 SER
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   70 ILE
Chi-restraints excluded: chain F residue   77 ASN
Chi-restraints excluded: chain F residue  148 THR
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  238 SER
Chi-restraints excluded: chain F residue  256 CYS
Chi-restraints excluded: chain F residue  303 THR
Chi-restraints excluded: chain F residue  324 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 25 optimal weight:    0.6980
   chunk 14 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 9 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
F  77 ASN
** F 136 GLN ** 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 = 0.3461 r_free = 0.3461 target = 0.127097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.112771 restraints weight = 4294.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 1.80
r_work: 0.3191 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.4694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3014  Z= 0.131
  Angle     :  0.628   6.922   4089  Z= 0.304
  Chirality :  0.044   0.152    453
  Planarity :  0.004   0.031    523
  Dihedral  :  7.360  92.631    420
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 20.25 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.44), residues: 369
  helix:  1.22 (0.44), residues: 143
  sheet:  0.85 (0.63), residues: 60
  loop : -0.90 (0.48), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F  78 
 HIS   0.003   0.001   HIS F 100 
 PHE   0.013   0.001   PHE F 254 
 TYR   0.009   0.001   TYR F 293 
 ARG   0.002   0.000   ARG F 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03094 (  138)
  hydrogen bonds       : angle       4.18537 (  366)
  SS BOND              : bond        0.00154 (    1)
  SS BOND              : angle       1.01332 (    2)
  covalent geometry    : bond        0.00315 ( 3013)
  covalent geometry    : angle       0.62735 ( 4087)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 44
  time to evaluate  : 0.321 
Fit side-chains
REVERT: F  110 ASN cc_start: 0.8219 (m110) cc_final: 0.7982 (m110)
REVERT: F  282 MET cc_start: 0.8254 (mmm) cc_final: 0.8007 (mmm)
REVERT: F  324 MET cc_start: 0.3952 (OUTLIER) cc_final: 0.3671 (tpp)
REVERT: F  354 MET cc_start: 0.7961 (mmm) cc_final: 0.7663 (mpp)
REVERT: F  370 HIS cc_start: 0.8472 (m-70) cc_final: 0.8234 (m90)
  outliers start: 13
  outliers final: 10
  residues processed: 52
  average time/residue: 0.1058
  time to fit residues: 7.2556
Evaluate side-chains
  57 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   13 SER
Chi-restraints excluded: chain F residue   53 VAL
Chi-restraints excluded: chain F residue   70 ILE
Chi-restraints excluded: chain F residue   77 ASN
Chi-restraints excluded: chain F residue  148 THR
Chi-restraints excluded: chain F residue  178 ASP
Chi-restraints excluded: chain F residue  238 SER
Chi-restraints excluded: chain F residue  240 GLU
Chi-restraints excluded: chain F residue  256 CYS
Chi-restraints excluded: chain F residue  303 THR
Chi-restraints excluded: chain F residue  324 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0470
   chunk 35 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 33 optimal weight:    0.2980
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
F  77 ASN
** F 136 GLN ** 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 = 0.3471 r_free = 0.3471 target = 0.128074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.113848 restraints weight = 4174.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.77
r_work: 0.3211 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3094 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.4761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3014  Z= 0.117
  Angle     :  0.619   6.910   4089  Z= 0.298
  Chirality :  0.044   0.157    453
  Planarity :  0.004   0.030    523
  Dihedral  :  7.305  91.509    420
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 20.25 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.44), residues: 369
  helix:  1.32 (0.44), residues: 143
  sheet:  0.84 (0.64), residues: 60
  loop : -0.87 (0.48), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F  78 
 HIS   0.003   0.001   HIS F 100 
 PHE   0.013   0.001   PHE F 254 
 TYR   0.009   0.001   TYR F 293 
 ARG   0.001   0.000   ARG F 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02915 (  138)
  hydrogen bonds       : angle       4.15246 (  366)
  SS BOND              : bond        0.00109 (    1)
  SS BOND              : angle       0.83191 (    2)
  covalent geometry    : bond        0.00278 ( 3013)
  covalent geometry    : angle       0.61857 ( 4087)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1915.46 seconds
wall clock time: 33 minutes 32.27 seconds (2012.27 seconds total)