Starting phenix.real_space_refine
on Fri Aug 22 12:54:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j27_35946/08_2025/8j27_35946.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j27_35946/08_2025/8j27_35946.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j27_35946/08_2025/8j27_35946.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j27_35946/08_2025/8j27_35946.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j27_35946/08_2025/8j27_35946.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j27_35946/08_2025/8j27_35946.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S       8      5.16       5
     C    1500      2.51       5
     N     425      2.21       5
     O     458      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 2393
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "F"
      Number of atoms: 99
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 99
          Classifications: {'peptide': 12}
          Link IDs: {'TRANS': 11}
    Chain: "A"
      Number of atoms: 138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 138
          Classifications: {'peptide': 16}
          Link IDs: {'TRANS': 15}
    Chain: "B"
      Number of atoms: 2001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2001
          Classifications: {'peptide': 264}
          Link IDs: {'PTRANS': 4, 'TRANS': 259}
          Chain breaks: 3
    Chain: "E"
      Number of atoms: 128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 128
          Classifications: {'peptide': 15}
          Link IDs: {'TRANS': 14}
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.71, per 1000 atoms: 0.30
  Number of scatterers: 2393
  At special positions: 0
  Unit cell: (67.84, 68.9, 78.44, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       8     16.00
     P       2     15.00
     O     458      8.00
     N     425      7.00
     C    1500      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: 0.14
  Conformation dependent library (CDL) restraints added in 55.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  564

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 1 sheets defined
      54.7% alpha, 10.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing helix  chain 'F' and resid 72 through 77
    Processing helix  chain 'A' and resid 70 through 78
    Processing helix  chain 'A' and resid 79 through 83
    Processing helix  chain 'B' and resid 8 through 12
      removed outlier: 3.511A  pdb=" N   LYS B  12 " --> pdb=" O   ALA B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 27
    Processing helix  chain 'B' and resid 28 through 32
    Processing helix  chain 'B' and resid 34 through 50
    Processing helix  chain 'B' and resid 61 through 77
      removed outlier: 3.591A  pdb=" N   LEU B  65 " --> pdb=" O   GLY B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 112
    Processing helix  chain 'B' and resid 113 through 115
      No H-bonds generated for 'chain 'B' and resid 113 through 115'
    Processing helix  chain 'B' and resid 124 through 128
      removed outlier: 3.761A  pdb=" N   PHE B 128 " --> pdb=" O   ASP B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 145
    Processing helix  chain 'B' and resid 171 through 174
    Processing helix  chain 'B' and resid 175 through 187
    Processing helix  chain 'B' and resid 218 through 223
    Processing helix  chain 'B' and resid 241 through 251
    Processing helix  chain 'B' and resid 265 through 271
    Processing helix  chain 'E' and resid 72 through 77
    Processing helix  chain 'E' and resid 79 through 85
      removed outlier: 3.554A  pdb=" N   LYS E  85 " --> pdb=" O   ALA E  81 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 118 through 123
      removed outlier: 3.932A  pdb=" N   ASN B 154 " --> pdb=" O   MET B 121 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL B 123 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   VAL B  55 " --> pdb=" O   PRO B 151 " (cutoff:3.500A)
      removed outlier: 8.805A  pdb=" N   PHE B 153 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   LEU B  57 " --> pdb=" O   PHE B 153 " (cutoff:3.500A)
      removed outlier: 8.744A  pdb=" N   GLU B 155 " --> pdb=" O   LEU B  57 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   ARG B  16 " --> pdb=" O   LEU B 191 " (cutoff:3.500A)
      removed outlier: 8.218A  pdb=" N   ILE B 193 " --> pdb=" O   ARG B  16 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   VAL B  18 " --> pdb=" O   ILE B 193 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   LEU B 195 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LYS B  20 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
      removed outlier: 8.262A  pdb=" N   ILE B 257 " --> pdb=" O   ASP B 190 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   LEU B 192 " --> pdb=" O   ILE B 257 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   THR B 259 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 5.761A  pdb=" N   LEU B 194 " --> pdb=" O   THR B 259 " (cutoff:3.500A)

    106 hydrogen bonds defined for protein.
    291 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: 0.19

  Time building geometry restraints manager: 0.17 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 404
        1.32 -     1.44: 617
        1.44 -     1.56: 1382
        1.56 -     1.68: 3
        1.68 -     1.81: 14
  Bond restraints: 2420
  Sorted by residual:
  bond pdb=" C   CYS B  95 "
       pdb=" O   CYS B  95 "
    ideal  model  delta    sigma   weight residual
    1.236  1.197  0.040 1.15e-02 7.56e+03 1.19e+01
  bond pdb=" N   ALA E  81 "
       pdb=" CA  ALA E  81 "
    ideal  model  delta    sigma   weight residual
    1.459  1.425  0.034 1.23e-02 6.61e+03 7.65e+00
  bond pdb=" C   GLY B  97 "
       pdb=" O   GLY B  97 "
    ideal  model  delta    sigma   weight residual
    1.235  1.271 -0.037 1.35e-02 5.49e+03 7.41e+00
  bond pdb=" C   ALA B  94 "
       pdb=" O   ALA B  94 "
    ideal  model  delta    sigma   weight residual
    1.236  1.271 -0.035 1.28e-02 6.10e+03 7.37e+00
  bond pdb=" N   CYS B  95 "
       pdb=" CA  CYS B  95 "
    ideal  model  delta    sigma   weight residual
    1.459  1.427  0.032 1.19e-02 7.06e+03 7.16e+00
  ... (remaining 2415 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 3010
        1.56 -     3.13: 194
        3.13 -     4.69: 37
        4.69 -     6.25: 13
        6.25 -     7.81: 3
  Bond angle restraints: 3257
  Sorted by residual:
  angle pdb=" N   CYS B  95 "
        pdb=" CA  CYS B  95 "
        pdb=" C   CYS B  95 "
      ideal   model   delta    sigma   weight residual
     111.07  104.19    6.88 1.07e+00 8.73e-01 4.13e+01
  angle pdb=" N   PHE F  80 "
        pdb=" CA  PHE F  80 "
        pdb=" C   PHE F  80 "
      ideal   model   delta    sigma   weight residual
     111.75  103.94    7.81 1.28e+00 6.10e-01 3.73e+01
  angle pdb=" N   ALA B  81 "
        pdb=" CA  ALA B  81 "
        pdb=" C   ALA B  81 "
      ideal   model   delta    sigma   weight residual
     112.87  106.75    6.12 1.20e+00 6.94e-01 2.60e+01
  angle pdb=" C   GLN B 100 "
        pdb=" N   SER B 101 "
        pdb=" CA  SER B 101 "
      ideal   model   delta    sigma   weight residual
     120.54  113.99    6.55 1.35e+00 5.49e-01 2.36e+01
  angle pdb=" N   GLY B  64 "
        pdb=" CA  GLY B  64 "
        pdb=" C   GLY B  64 "
      ideal   model   delta    sigma   weight residual
     112.50  117.73   -5.23 1.16e+00 7.43e-01 2.03e+01
  ... (remaining 3252 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.68: 1343
       25.68 -    51.35: 103
       51.35 -    77.03: 6
       77.03 -   102.70: 1
      102.70 -   128.38: 2
  Dihedral angle restraints: 1455
    sinusoidal: 582
      harmonic: 873
  Sorted by residual:
  dihedral pdb=" O1B ADP B 801 "
           pdb=" O3A ADP B 801 "
           pdb=" PB  ADP B 801 "
           pdb=" PA  ADP B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   68.38 -128.38     1      2.00e+01 2.50e-03 3.89e+01
  dihedral pdb=" C5' ADP B 801 "
           pdb=" O5' ADP B 801 "
           pdb=" PA  ADP B 801 "
           pdb=" O2A ADP B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   61.59 -121.59     1      2.00e+01 2.50e-03 3.66e+01
  dihedral pdb=" CA  ASP B 115 "
           pdb=" CB  ASP B 115 "
           pdb=" CG  ASP B 115 "
           pdb=" OD1 ASP B 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.59   57.59     1      2.00e+01 2.50e-03 1.11e+01
  ... (remaining 1452 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 197
       0.028 -    0.056: 107
       0.056 -    0.083: 40
       0.083 -    0.111: 22
       0.111 -    0.139: 13
  Chirality restraints: 379
  Sorted by residual:
  chirality pdb=" CA  ILE B  56 "
            pdb=" N   ILE B  56 "
            pdb=" C   ILE B  56 "
            pdb=" CB  ILE B  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.82e-01
  chirality pdb=" CB  ILE B 226 "
            pdb=" CA  ILE B 226 "
            pdb=" CG1 ILE B 226 "
            pdb=" CG2 ILE B 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.77e-01
  chirality pdb=" CA  ILE B 258 "
            pdb=" N   ILE B 258 "
            pdb=" C   ILE B 258 "
            pdb=" CB  ILE B 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.77e-01
  ... (remaining 376 not shown)

  Planarity restraints: 411
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B  80 "   -0.010 2.00e-02 2.50e+03   2.03e-02 4.13e+00
        pdb=" C   PHE B  80 "    0.035 2.00e-02 2.50e+03
        pdb=" O   PHE B  80 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ALA B  81 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B  43 "    0.007 2.00e-02 2.50e+03   1.33e-02 1.77e+00
        pdb=" CD  GLU B  43 "   -0.023 2.00e-02 2.50e+03
        pdb=" OE1 GLU B  43 "    0.008 2.00e-02 2.50e+03
        pdb=" OE2 GLU B  43 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B  95 "   -0.006 2.00e-02 2.50e+03   1.11e-02 1.24e+00
        pdb=" C   CYS B  95 "    0.019 2.00e-02 2.50e+03
        pdb=" O   CYS B  95 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ALA B  96 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 408 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 543
        2.77 -     3.30: 2473
        3.30 -     3.83: 3799
        3.83 -     4.37: 4318
        4.37 -     4.90: 7019
  Nonbonded interactions: 18152
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  60 "
            pdb=" ND2 ASN B 176 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" OE2 GLU B 199 "
            pdb=" OH  TYR B 202 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" N   GLU B 199 "
            pdb=" OE1 GLU B 199 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" O   SER F  79 "
            pdb=" N   ASP F  82 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" NH1 ARG B 134 "
            pdb=" OE1 GLU B 186 "
     model   vdw
     2.318 3.120
  ... (remaining 18147 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 71 through 84)
  selection = (chain 'E' and resid 71 through 84)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.680
  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:          0.030
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     2.880
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    4.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
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      :  0.006   0.040   2420  Z= 0.420
  Angle     :  0.896   7.813   3257  Z= 0.590
  Chirality :  0.047   0.139    379
  Planarity :  0.003   0.020    411
  Dihedral  : 17.193 128.380    891
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 25.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 31.89 %
    Favored  : 63.39 %
  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: -1.70 (0.47), residues: 293
  helix: -1.19 (0.41), residues: 144
  sheet:  1.21 (0.87), residues: 37
  loop : -1.72 (0.54), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B   8 
 TYR   0.007   0.001   TYR B 107 
 PHE   0.011   0.002   PHE B 280 
 TRP   0.013   0.003   TRP B 174 
 HIS   0.003   0.001   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00608 ( 2420)
  covalent geometry    : angle       0.89624 ( 3257)
  hydrogen bonds       : bond        0.20460 (  106)
  hydrogen bonds       : angle       7.66395 (  291)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 SER cc_start: 0.9393 (m) cc_final: 0.8955 (t)
  outliers start: 12
  outliers final: 3
  residues processed: 96
  average time/residue: 0.0394
  time to fit residues: 4.5375
Evaluate side-chains
  81 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain E residue   75 LEU
Chi-restraints excluded: chain E residue   80 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 24 optimal weight:    4.9990
   chunk 28 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0570
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.7500

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

Flipped N/Q/H residues before XYZ refinement:
F  77 ASN
B 120 GLN
B 222 HIS
B 223 GLN
E  84 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.110446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.095118 restraints weight = 7747.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.097783 restraints weight = 4506.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.099687 restraints weight = 3090.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.101073 restraints weight = 2316.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.102054 restraints weight = 1848.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2420  Z= 0.147
  Angle     :  0.721   6.226   3257  Z= 0.351
  Chirality :  0.044   0.166    379
  Planarity :  0.004   0.025    411
  Dihedral  : 10.887 117.121    347
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 14.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 29.53 %
    Favored  : 65.35 %
  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: -0.55 (0.48), residues: 293
  helix:  0.20 (0.44), residues: 134
  sheet:  1.01 (0.86), residues: 39
  loop : -1.46 (0.55), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E  71 
 TYR   0.025   0.002   TYR E  72 
 PHE   0.021   0.002   PHE F  80 
 TRP   0.007   0.002   TRP B 174 
 HIS   0.001   0.000   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 2420)
  covalent geometry    : angle       0.72053 ( 3257)
  hydrogen bonds       : bond        0.04607 (  106)
  hydrogen bonds       : angle       4.82393 (  291)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.056 
Fit side-chains
REVERT: F   72 TYR cc_start: 0.7763 (t80) cc_final: 0.7450 (t80)
REVERT: A   78 SER cc_start: 0.9277 (m) cc_final: 0.8952 (t)
REVERT: B   72 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7291 (t80)
REVERT: B  144 MET cc_start: 0.9163 (ttt) cc_final: 0.8504 (tmm)
REVERT: B  225 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8308 (pp20)
  outliers start: 13
  outliers final: 7
  residues processed: 84
  average time/residue: 0.0277
  time to fit residues: 2.9449
Evaluate side-chains
  76 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain E residue   75 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 7 optimal weight:    8.9990
   chunk 11 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    0.8980
   chunk 28 optimal weight:   10.0000
   chunk 17 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** E  74 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 = 0.3707 r_free = 0.3707 target = 0.108671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.093397 restraints weight = 7992.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.096028 restraints weight = 4746.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.097935 restraints weight = 3250.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.099086 restraints weight = 2433.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.100240 restraints weight = 1974.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2420  Z= 0.157
  Angle     :  0.733   6.027   3257  Z= 0.350
  Chirality :  0.044   0.158    379
  Planarity :  0.003   0.016    411
  Dihedral  : 10.529 115.102    344
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 31.10 %
    Favored  : 62.60 %
  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: -0.30 (0.47), residues: 293
  helix:  0.54 (0.41), residues: 136
  sheet:  1.13 (0.89), residues: 40
  loop : -1.55 (0.54), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  71 
 TYR   0.007   0.001   TYR A  72 
 PHE   0.007   0.001   PHE B 153 
 TRP   0.005   0.001   TRP B 174 
 HIS   0.002   0.001   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 2420)
  covalent geometry    : angle       0.73319 ( 3257)
  hydrogen bonds       : bond        0.04040 (  106)
  hydrogen bonds       : angle       4.72848 (  291)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 SER cc_start: 0.9374 (m) cc_final: 0.9174 (t)
REVERT: B   44 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8879 (pp30)
REVERT: B   72 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7651 (t80)
REVERT: B  144 MET cc_start: 0.9177 (ttt) cc_final: 0.8530 (tmm)
  outliers start: 16
  outliers final: 9
  residues processed: 83
  average time/residue: 0.0331
  time to fit residues: 3.3449
Evaluate side-chains
  82 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  129 ARG
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  267 ILE
Chi-restraints excluded: chain B residue  276 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 28 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 1 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** E  74 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 = 0.3686 r_free = 0.3686 target = 0.107468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.092250 restraints weight = 8136.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.094772 restraints weight = 4822.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.096603 restraints weight = 3348.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.097907 restraints weight = 2542.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.098917 restraints weight = 2050.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.3820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2420  Z= 0.162
  Angle     :  0.750   8.381   3257  Z= 0.349
  Chirality :  0.044   0.152    379
  Planarity :  0.003   0.017    411
  Dihedral  : 10.326 113.253    342
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 30.71 %
    Favored  : 64.57 %
  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: -0.25 (0.48), residues: 293
  helix:  0.72 (0.41), residues: 137
  sheet:  1.07 (0.90), residues: 40
  loop : -1.72 (0.54), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  73 
 TYR   0.016   0.001   TYR F  72 
 PHE   0.010   0.001   PHE F  80 
 TRP   0.005   0.001   TRP B 174 
 HIS   0.002   0.001   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 2420)
  covalent geometry    : angle       0.75032 ( 3257)
  hydrogen bonds       : bond        0.04022 (  106)
  hydrogen bonds       : angle       4.68519 (  291)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.057 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8784 (pp30)
REVERT: B   72 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.7730 (t80)
REVERT: B  144 MET cc_start: 0.9162 (ttt) cc_final: 0.8553 (tmm)
  outliers start: 12
  outliers final: 7
  residues processed: 76
  average time/residue: 0.0300
  time to fit residues: 2.8635
Evaluate side-chains
  78 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 GLU
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  129 ARG
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  276 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 24 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0270
   chunk 8 optimal weight:    0.8980
   overall best weight:    1.3242

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
B 120 GLN
** E  74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.108358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.093097 restraints weight = 7948.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.095714 restraints weight = 4758.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.097538 restraints weight = 3307.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.098866 restraints weight = 2512.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.099880 restraints weight = 2023.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.4120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2420  Z= 0.143
  Angle     :  0.729   6.272   3257  Z= 0.340
  Chirality :  0.043   0.153    379
  Planarity :  0.003   0.016    411
  Dihedral  : 10.162 109.331    342
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  6.69 %
    Allowed  : 30.31 %
    Favored  : 62.99 %
  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: -0.09 (0.49), residues: 293
  helix:  0.96 (0.43), residues: 137
  sheet:  1.21 (0.92), residues: 40
  loop : -1.81 (0.53), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  71 
 TYR   0.010   0.001   TYR F  72 
 PHE   0.005   0.001   PHE B 153 
 TRP   0.005   0.001   TRP B 174 
 HIS   0.002   0.001   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 2420)
  covalent geometry    : angle       0.72930 ( 3257)
  hydrogen bonds       : bond        0.03749 (  106)
  hydrogen bonds       : angle       4.57388 (  291)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.061 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   44 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8863 (pp30)
REVERT: B   72 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.7814 (t80)
REVERT: B  120 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8396 (pp30)
REVERT: B  144 MET cc_start: 0.9095 (ttt) cc_final: 0.8535 (tmm)
  outliers start: 17
  outliers final: 10
  residues processed: 79
  average time/residue: 0.0398
  time to fit residues: 3.8919
Evaluate side-chains
  82 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  120 GLN
Chi-restraints excluded: chain B residue  129 ARG
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  276 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 16 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 120 GLN
E  74 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.108650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.093268 restraints weight = 7987.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.095973 restraints weight = 4801.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.097828 restraints weight = 3317.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.099188 restraints weight = 2509.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.100198 restraints weight = 2014.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.4392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2420  Z= 0.138
  Angle     :  0.739   6.599   3257  Z= 0.344
  Chirality :  0.043   0.148    379
  Planarity :  0.003   0.015    411
  Dihedral  :  9.973 104.970    342
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 34.25 %
    Favored  : 60.24 %
  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: -0.06 (0.49), residues: 293
  helix:  1.06 (0.43), residues: 137
  sheet:  1.19 (0.92), residues: 40
  loop : -1.90 (0.54), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  71 
 TYR   0.007   0.001   TYR F  72 
 PHE   0.011   0.001   PHE F  80 
 TRP   0.006   0.002   TRP B 174 
 HIS   0.002   0.000   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 2420)
  covalent geometry    : angle       0.73924 ( 3257)
  hydrogen bonds       : bond        0.03707 (  106)
  hydrogen bonds       : angle       4.61267 (  291)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: B   44 GLN cc_start: 0.9081 (tm-30) cc_final: 0.8847 (pp30)
REVERT: B   72 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.7830 (t80)
REVERT: B  120 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8346 (pp30)
REVERT: B  139 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8700 (tm-30)
REVERT: B  144 MET cc_start: 0.9153 (ttt) cc_final: 0.8609 (tmm)
  outliers start: 14
  outliers final: 9
  residues processed: 80
  average time/residue: 0.0402
  time to fit residues: 4.1619
Evaluate side-chains
  81 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  120 GLN
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  276 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 26 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   chunk 4 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 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 = 0.3711 r_free = 0.3711 target = 0.108867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.093356 restraints weight = 7957.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.096042 restraints weight = 4843.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.097840 restraints weight = 3387.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.099175 restraints weight = 2585.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.100196 restraints weight = 2091.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.4535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   2420  Z= 0.145
  Angle     :  0.764   8.102   3257  Z= 0.354
  Chirality :  0.043   0.154    379
  Planarity :  0.003   0.014    411
  Dihedral  :  9.768  99.014    342
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 38.19 %
    Favored  : 56.69 %
  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: -0.13 (0.49), residues: 293
  helix:  0.99 (0.43), residues: 137
  sheet:  1.06 (0.92), residues: 40
  loop : -1.88 (0.54), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  71 
 TYR   0.007   0.001   TYR F  72 
 PHE   0.007   0.001   PHE B 153 
 TRP   0.006   0.002   TRP B 174 
 HIS   0.002   0.001   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 2420)
  covalent geometry    : angle       0.76445 ( 3257)
  hydrogen bonds       : bond        0.03672 (  106)
  hydrogen bonds       : angle       4.64907 (  291)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
REVERT: B   44 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8839 (pp30)
REVERT: B   72 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7849 (t80)
REVERT: B  139 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8658 (tm-30)
REVERT: B  144 MET cc_start: 0.9105 (ttt) cc_final: 0.8559 (tmm)
  outliers start: 13
  outliers final: 10
  residues processed: 76
  average time/residue: 0.0461
  time to fit residues: 4.3808
Evaluate side-chains
  80 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  129 ARG
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  276 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 23 optimal weight:    0.3980
   chunk 22 optimal weight:    7.9990
   chunk 5 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 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 = 0.3738 r_free = 0.3738 target = 0.110272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.094739 restraints weight = 8000.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.097461 restraints weight = 4839.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.099266 restraints weight = 3369.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.100650 restraints weight = 2561.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.101525 restraints weight = 2062.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.4810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   2420  Z= 0.135
  Angle     :  0.776   7.821   3257  Z= 0.356
  Chirality :  0.043   0.159    379
  Planarity :  0.003   0.014    411
  Dihedral  :  9.511 112.732    342
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 39.37 %
    Favored  : 55.51 %
  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:  0.06 (0.50), residues: 293
  helix:  1.16 (0.44), residues: 136
  sheet:  1.05 (0.91), residues: 40
  loop : -1.73 (0.56), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  71 
 TYR   0.022   0.002   TYR F  72 
 PHE   0.012   0.001   PHE F  80 
 TRP   0.007   0.002   TRP B 174 
 HIS   0.001   0.000   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 2420)
  covalent geometry    : angle       0.77589 ( 3257)
  hydrogen bonds       : bond        0.03486 (  106)
  hydrogen bonds       : angle       4.61898 (  291)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
REVERT: B   44 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8808 (pp30)
REVERT: B   72 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.7794 (t80)
REVERT: B  110 MET cc_start: 0.6580 (tpt) cc_final: 0.6332 (ttm)
REVERT: B  144 MET cc_start: 0.9126 (ttt) cc_final: 0.8593 (tmm)
  outliers start: 13
  outliers final: 8
  residues processed: 79
  average time/residue: 0.0497
  time to fit residues: 4.8727
Evaluate side-chains
  76 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  129 ARG
Chi-restraints excluded: chain B residue  157 ASP
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  276 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 20 optimal weight:    0.0020
   chunk 7 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 24 optimal weight:    0.0570
   chunk 27 optimal weight:    0.0770
   chunk 8 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 28 optimal weight:   10.0000
   overall best weight:    0.6266

-------------------------------------------------------------------------------
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 = 0.3748 r_free = 0.3748 target = 0.111404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.095568 restraints weight = 8084.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.098278 restraints weight = 4897.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.100142 restraints weight = 3429.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.101542 restraints weight = 2611.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.102632 restraints weight = 2100.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.5013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   2420  Z= 0.136
  Angle     :  0.835   8.700   3257  Z= 0.379
  Chirality :  0.043   0.151    379
  Planarity :  0.002   0.013    411
  Dihedral  :  9.620 126.835    342
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 39.76 %
    Favored  : 56.30 %
  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:  0.24 (0.50), residues: 293
  helix:  1.24 (0.44), residues: 136
  sheet:  1.45 (0.96), residues: 40
  loop : -1.68 (0.56), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  71 
 TYR   0.012   0.001   TYR E  72 
 PHE   0.006   0.001   PHE A  80 
 TRP   0.007   0.002   TRP B 174 
 HIS   0.002   0.000   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 2420)
  covalent geometry    : angle       0.83502 ( 3257)
  hydrogen bonds       : bond        0.03400 (  106)
  hydrogen bonds       : angle       4.62051 (  291)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
REVERT: B   44 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8783 (pp30)
REVERT: B   72 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.7818 (t80)
REVERT: B  110 MET cc_start: 0.6573 (tpt) cc_final: 0.6361 (ttm)
REVERT: B  144 MET cc_start: 0.9123 (ttt) cc_final: 0.8538 (tmm)
REVERT: B  147 MET cc_start: 0.8142 (ptp) cc_final: 0.7893 (pmm)
REVERT: B  174 TRP cc_start: 0.7756 (t60) cc_final: 0.7417 (t60)
  outliers start: 10
  outliers final: 8
  residues processed: 80
  average time/residue: 0.0491
  time to fit residues: 4.8836
Evaluate side-chains
  79 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  129 ARG
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  214 ILE
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  276 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0050
   chunk 21 optimal weight:    0.2980
   chunk 16 optimal weight:    5.9990
   chunk 20 optimal weight:    0.2980
   chunk 2 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.4994

-------------------------------------------------------------------------------
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 = 0.3763 r_free = 0.3763 target = 0.112355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.096471 restraints weight = 8154.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.099220 restraints weight = 4950.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.101117 restraints weight = 3456.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.102546 restraints weight = 2622.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.103646 restraints weight = 2105.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.5235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   2420  Z= 0.136
  Angle     :  0.838   8.806   3257  Z= 0.379
  Chirality :  0.043   0.166    379
  Planarity :  0.002   0.014    411
  Dihedral  :  9.544 127.413    342
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 40.55 %
    Favored  : 55.91 %
  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:  0.25 (0.50), residues: 293
  helix:  1.21 (0.44), residues: 137
  sheet:  1.40 (0.93), residues: 40
  loop : -1.63 (0.57), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  71 
 TYR   0.023   0.001   TYR E  72 
 PHE   0.013   0.001   PHE F  80 
 TRP   0.008   0.002   TRP B 174 
 HIS   0.001   0.000   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 2420)
  covalent geometry    : angle       0.83807 ( 3257)
  hydrogen bonds       : bond        0.03308 (  106)
  hydrogen bonds       : angle       4.57896 (  291)

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

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

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  586 Ramachandran restraints generated.
    293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: B   44 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8810 (pp30)
REVERT: B   72 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7829 (t80)
REVERT: B  144 MET cc_start: 0.9085 (ttt) cc_final: 0.8433 (tmm)
REVERT: B  174 TRP cc_start: 0.7728 (t60) cc_final: 0.7228 (t60)
  outliers start: 9
  outliers final: 6
  residues processed: 79
  average time/residue: 0.0599
  time to fit residues: 5.7216
Evaluate side-chains
  77 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   72 TYR
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  129 ARG
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  209 SER
Chi-restraints excluded: chain B residue  276 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 1 optimal weight:    0.7980
   chunk 13 optimal weight:    9.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3744 r_free = 0.3744 target = 0.111005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.095097 restraints weight = 8191.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.097821 restraints weight = 5031.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.099557 restraints weight = 3539.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.101045 restraints weight = 2737.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.102070 restraints weight = 2201.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.5256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   2420  Z= 0.144
  Angle     :  0.839   8.275   3257  Z= 0.385
  Chirality :  0.043   0.155    379
  Planarity :  0.003   0.021    411
  Dihedral  :  9.352 125.856    342
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 41.73 %
    Favored  : 55.51 %
  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:  0.14 (0.50), residues: 293
  helix:  1.09 (0.43), residues: 138
  sheet:  1.48 (0.92), residues: 40
  loop : -1.73 (0.57), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  71 
 TYR   0.019   0.002   TYR F  72 
 PHE   0.006   0.001   PHE B 153 
 TRP   0.007   0.002   TRP B 174 
 HIS   0.001   0.000   HIS B 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 2420)
  covalent geometry    : angle       0.83939 ( 3257)
  hydrogen bonds       : bond        0.03502 (  106)
  hydrogen bonds       : angle       4.54787 (  291)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 591.63 seconds
wall clock time: 10 minutes 57.86 seconds (657.86 seconds total)