Starting phenix.real_space_refine
on Wed Sep 17 05:22:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9h1s_51771/09_2025/9h1s_51771.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9h1s_51771/09_2025/9h1s_51771.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9h1s_51771/09_2025/9h1s_51771.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9h1s_51771/09_2025/9h1s_51771.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9h1s_51771/09_2025/9h1s_51771.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9h1s_51771/09_2025/9h1s_51771.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      28      5.16       5
     C    3140      2.51       5
     N     882      2.21       5
     O     942      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4994
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2496
          Classifications: {'peptide': 308}
          Link IDs: {'PTRANS': 14, 'TRANS': 293}
    Chain: "B"
      Number of atoms: 2496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2496
          Classifications: {'peptide': 308}
          Link IDs: {'PTRANS': 14, 'TRANS': 293}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM     43  SG  CYS A  18      39.775  17.296  45.776  1.00172.16           S
  ATOM    179  SG  CYS A  36      39.437  16.084  43.598  1.00208.25           S
  ATOM    286  SG  CYS A  49      41.664  17.292  43.752  1.00159.54           S
  ATOM   2539  SG  CYS B  18      88.798  19.950  32.780  1.00179.22           S
  ATOM   2675  SG  CYS B  36      89.836  17.890  33.887  1.00210.11           S
  ATOM   2782  SG  CYS B  49      87.570  18.854  34.806  1.00165.98           S

  Time building chain proxies: 1.34, per 1000 atoms: 0.27
  Number of scatterers: 4994
  At special positions: 0
  Unit cell: (129.6, 59.4, 78.3, 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)
     Zn      2     29.99
     S      28     16.00
     O     942      8.00
     N     882      7.00
     C    3140      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: 0.34
  Conformation dependent library (CDL) restraints added in 184.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 401 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A  49 "
        pdb="ZN    ZN A 401 " - pdb=" NE2 HIS A  52 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A  18 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A  36 "
      pdb="  ZN B 401 "
        pdb="ZN    ZN B 401 " - pdb=" NE2 HIS B  52 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS B  18 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS B  49 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS B  36 "
      Number of angles added : 6


  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1180

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 7 sheets defined
      37.5% alpha, 10.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 23
    Processing helix  chain 'A' and resid 37 through 42
    Processing helix  chain 'A' and resid 49 through 58
    Processing helix  chain 'A' and resid 88 through 91
    Processing helix  chain 'A' and resid 100 through 105
    Processing helix  chain 'A' and resid 106 through 110
    Processing helix  chain 'A' and resid 111 through 122
    Processing helix  chain 'A' and resid 124 through 136
    Processing helix  chain 'A' and resid 144 through 164
    Processing helix  chain 'A' and resid 181 through 186
    Processing helix  chain 'A' and resid 191 through 199
    Processing helix  chain 'A' and resid 201 through 212
    Processing helix  chain 'A' and resid 278 through 285
    Processing helix  chain 'B' and resid 37 through 42
    Processing helix  chain 'B' and resid 49 through 58
    Processing helix  chain 'B' and resid 88 through 91
    Processing helix  chain 'B' and resid 100 through 105
    Processing helix  chain 'B' and resid 106 through 110
    Processing helix  chain 'B' and resid 111 through 122
    Processing helix  chain 'B' and resid 124 through 137
      removed outlier: 3.995A  pdb=" N   TYR B 137 " --> pdb=" O   ASP B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 164
    Processing helix  chain 'B' and resid 181 through 186
    Processing helix  chain 'B' and resid 190 through 198
    Processing helix  chain 'B' and resid 201 through 212
    Processing helix  chain 'B' and resid 278 through 285
    Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 67
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 96
    Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 179
      removed outlier: 6.359A  pdb=" N   TYR A 216 " --> pdb=" O   GLN A 302 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   ILE A 304 " --> pdb=" O   TYR A 216 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   GLN A 218 " --> pdb=" O   ILE A 304 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 290
      removed outlier: 6.684A  pdb=" N   GLU A 289 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 67
    Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 96
      removed outlier: 6.450A  pdb=" N   LEU B 239 " --> pdb=" O   LEU B  94 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 176 through 179
      removed outlier: 6.350A  pdb=" N   TYR B 216 " --> pdb=" O   GLN B 302 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   ILE B 304 " --> pdb=" O   TYR B 216 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   GLN B 218 " --> pdb=" O   ILE B 304 " (cutoff:3.500A)

    178 hydrogen bonds defined for protein.
    462 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: 0.70

  Time building geometry restraints manager: 0.50 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1480
        1.33 -     1.46: 1366
        1.46 -     1.59: 2210
        1.59 -     1.72: 0
        1.72 -     1.85: 40
  Bond restraints: 5096
  Sorted by residual:
  bond pdb=" CA  PHE A  67 "
       pdb=" C   PHE A  67 "
    ideal  model  delta    sigma   weight residual
    1.524  1.480  0.043 1.25e-02 6.40e+03 1.20e+01
  bond pdb=" CA  ILE A  93 "
       pdb=" C   ILE A  93 "
    ideal  model  delta    sigma   weight residual
    1.527  1.499  0.028 9.70e-03 1.06e+04 8.44e+00
  bond pdb=" N   VAL A 243 "
       pdb=" CA  VAL A 243 "
    ideal  model  delta    sigma   weight residual
    1.460  1.438  0.022 7.50e-03 1.78e+04 8.25e+00
  bond pdb=" CA  GLN A 218 "
       pdb=" C   GLN A 218 "
    ideal  model  delta    sigma   weight residual
    1.524  1.489  0.035 1.23e-02 6.61e+03 8.05e+00
  bond pdb=" CA  ILE A 219 "
       pdb=" C   ILE A 219 "
    ideal  model  delta    sigma   weight residual
    1.523  1.486  0.036 1.28e-02 6.10e+03 7.99e+00
  ... (remaining 5091 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 5957
        2.00 -     3.99: 796
        3.99 -     5.99: 114
        5.99 -     7.98: 25
        7.98 -     9.98: 14
  Bond angle restraints: 6906
  Sorted by residual:
  angle pdb=" C   GLY A 246 "
        pdb=" N   PRO A 247 "
        pdb=" CA  PRO A 247 "
      ideal   model   delta    sigma   weight residual
     119.90  128.92   -9.02 1.02e+00 9.61e-01 7.82e+01
  angle pdb=" C   SER B  37 "
        pdb=" N   PRO B  38 "
        pdb=" CA  PRO B  38 "
      ideal   model   delta    sigma   weight residual
     119.47  129.45   -9.98 1.16e+00 7.43e-01 7.40e+01
  angle pdb=" C   VAL A 295 "
        pdb=" N   PRO A 296 "
        pdb=" CA  PRO A 296 "
      ideal   model   delta    sigma   weight residual
     119.92  128.95   -9.03 1.07e+00 8.73e-01 7.13e+01
  angle pdb=" C   ASN B 164 "
        pdb=" N   PRO B 165 "
        pdb=" CA  PRO B 165 "
      ideal   model   delta    sigma   weight residual
     119.87  128.53   -8.66 1.04e+00 9.25e-01 6.94e+01
  angle pdb=" C   GLY B 246 "
        pdb=" N   PRO B 247 "
        pdb=" CA  PRO B 247 "
      ideal   model   delta    sigma   weight residual
     120.31  128.22   -7.91 9.80e-01 1.04e+00 6.51e+01
  ... (remaining 6901 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.46: 2980
       16.46 -    32.92: 78
       32.92 -    49.38: 24
       49.38 -    65.84: 6
       65.84 -    82.30: 4
  Dihedral angle restraints: 3092
    sinusoidal: 1272
      harmonic: 1820
  Sorted by residual:
  dihedral pdb=" C   ASN B 228 "
           pdb=" N   ASN B 228 "
           pdb=" CA  ASN B 228 "
           pdb=" CB  ASN B 228 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.46    7.86     0      2.50e+00 1.60e-01 9.89e+00
  dihedral pdb=" CB  GLU B 139 "
           pdb=" CG  GLU B 139 "
           pdb=" CD  GLU B 139 "
           pdb=" OE1 GLU B 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -78.95   78.95     1      3.00e+01 1.11e-03 8.62e+00
  dihedral pdb=" CB  GLU A  87 "
           pdb=" CG  GLU A  87 "
           pdb=" CD  GLU A  87 "
           pdb=" OE1 GLU A  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   70.88  -70.88     1      3.00e+01 1.11e-03 7.17e+00
  ... (remaining 3089 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 509
       0.073 -    0.147: 219
       0.147 -    0.220: 29
       0.220 -    0.294: 0
       0.294 -    0.367: 1
  Chirality restraints: 758
  Sorted by residual:
  chirality pdb=" CA  ASN B 228 "
            pdb=" N   ASN B 228 "
            pdb=" C   ASN B 228 "
            pdb=" CB  ASN B 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.37e+00
  chirality pdb=" CA  ASN A 100 "
            pdb=" N   ASN A 100 "
            pdb=" C   ASN A 100 "
            pdb=" CB  ASN A 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  ASN B 100 "
            pdb=" N   ASN B 100 "
            pdb=" C   ASN B 100 "
            pdb=" CB  ASN B 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.57e-01
  ... (remaining 755 not shown)

  Planarity restraints: 918
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 301 "   -0.035 2.00e-02 2.50e+03   1.82e-02 6.64e+00
        pdb=" CG  TYR A 301 "    0.017 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 301 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 301 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 301 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 301 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 301 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 301 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A  52 "   -0.025 2.00e-02 2.50e+03   1.93e-02 5.59e+00
        pdb=" CG  HIS A  52 "    0.024 2.00e-02 2.50e+03
        pdb=" ND1 HIS A  52 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 HIS A  52 "    0.019 2.00e-02 2.50e+03
        pdb=" CE1 HIS A  52 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE2 HIS A  52 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 200 "    0.029 2.00e-02 2.50e+03   1.63e-02 5.29e+00
        pdb=" CG  TYR B 200 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 200 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 200 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 200 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 200 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 200 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B 200 "    0.026 2.00e-02 2.50e+03
  ... (remaining 915 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1425
        2.80 -     3.32: 4908
        3.32 -     3.85: 8719
        3.85 -     4.37: 10280
        4.37 -     4.90: 16679
  Nonbonded interactions: 42011
  Sorted by model distance:
  nonbonded pdb=" N   GLU B  87 "
            pdb=" OE1 GLU B  87 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" N   GLU A 307 "
            pdb=" OE1 GLU A 307 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" N   GLN B 102 "
            pdb=" OE1 GLN B 102 "
     model   vdw
     2.374 3.120
  nonbonded pdb=" C   ASP B 245 "
            pdb=" OD1 ASP B 245 "
     model   vdw
     2.457 3.270
  nonbonded pdb=" OG  SER A 261 "
            pdb=" NE2 GLN A 262 "
     model   vdw
     2.470 3.120
  ... (remaining 42006 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     6.820
  Find NCS groups from input model:        0.080
  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:6.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
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      :  0.023   0.654   5104  Z= 1.076
  Angle     :  1.637  31.857   6912  Z= 1.064
  Chirality :  0.073   0.367    758
  Planarity :  0.006   0.036    918
  Dihedral  :  9.904  82.302   1912
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.11 (0.31), residues: 612
  helix: -0.57 (0.34), residues: 182
  sheet: -2.43 (0.70), residues: 40
  loop : -0.58 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 225 
 TYR   0.035   0.007   TYR A 301 
 PHE   0.019   0.004   PHE B 310 
 TRP   0.024   0.009   TRP A  46 
 HIS   0.013   0.003   HIS B  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.01411 ( 5096)
  covalent geometry    : angle       1.48218 ( 6906)
  hydrogen bonds       : bond        0.14570 (  178)
  hydrogen bonds       : angle       8.13432 (  462)
  metal coordination   : bond        0.45643 (    8)
  metal coordination   : angle      23.66946 (    6)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.8256 (ptp) cc_final: 0.6436 (ptt)
REVERT: A  114 GLU cc_start: 0.8211 (tt0) cc_final: 0.7756 (tt0)
REVERT: A  149 ILE cc_start: 0.8179 (mt) cc_final: 0.7731 (mt)
REVERT: A  157 LYS cc_start: 0.9365 (mmmt) cc_final: 0.9109 (tppp)
REVERT: A  219 ILE cc_start: 0.8882 (mt) cc_final: 0.8412 (mt)
REVERT: A  223 GLU cc_start: 0.8468 (tt0) cc_final: 0.7955 (tm-30)
REVERT: A  236 GLU cc_start: 0.9489 (pm20) cc_final: 0.9270 (pm20)
REVERT: A  257 ASP cc_start: 0.8922 (p0) cc_final: 0.8546 (p0)
REVERT: B   75 LYS cc_start: 0.8438 (mttt) cc_final: 0.8059 (mttt)
REVERT: B  110 MET cc_start: 0.8805 (ptp) cc_final: 0.8178 (ptt)
REVERT: B  114 GLU cc_start: 0.8053 (pt0) cc_final: 0.7712 (tt0)
REVERT: B  157 LYS cc_start: 0.9324 (mmmt) cc_final: 0.9076 (mmtm)
REVERT: B  215 GLU cc_start: 0.8311 (mp0) cc_final: 0.7942 (mp0)
REVERT: B  218 GLN cc_start: 0.8234 (tt0) cc_final: 0.7622 (tm-30)
REVERT: B  219 ILE cc_start: 0.8662 (mt) cc_final: 0.8448 (tt)
REVERT: B  223 GLU cc_start: 0.8585 (tt0) cc_final: 0.8114 (tm-30)
REVERT: B  236 GLU cc_start: 0.9424 (pm20) cc_final: 0.9203 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.7270
  time to fit residues: 107.7250
Evaluate side-chains
  72 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:    8.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    8.9990
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 58 optimal weight:    7.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  72 ASN
A 102 GLN
** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  42 HIS
** B  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 150 HIS
B 302 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.070747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.056053 restraints weight = 13166.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 4.22
r_work: 0.2864 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.3909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   5104  Z= 0.241
  Angle     :  0.702   7.686   6912  Z= 0.371
  Chirality :  0.047   0.158    758
  Planarity :  0.005   0.033    918
  Dihedral  :  4.958  20.773    688
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 10.57 %
    Favored  : 87.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.34), residues: 612
  helix:  0.32 (0.36), residues: 196
  sheet: -2.38 (0.83), residues: 40
  loop : -0.16 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 279 
 TYR   0.012   0.002   TYR A 288 
 PHE   0.017   0.002   PHE A 226 
 TRP   0.004   0.001   TRP A  46 
 HIS   0.012   0.003   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 ( 5096)
  covalent geometry    : angle       0.68714 ( 6906)
  hydrogen bonds       : bond        0.04546 (  178)
  hydrogen bonds       : angle       6.12947 (  462)
  metal coordination   : bond        0.02077 (    8)
  metal coordination   : angle       4.92447 (    6)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ASP cc_start: 0.8599 (t0) cc_final: 0.8366 (t0)
REVERT: A   87 GLU cc_start: 0.8806 (mp0) cc_final: 0.8275 (mp0)
REVERT: A  184 ASN cc_start: 0.8531 (m-40) cc_final: 0.8106 (t0)
REVERT: A  218 GLN cc_start: 0.8191 (tt0) cc_final: 0.7326 (tm130)
REVERT: A  235 ASP cc_start: 0.9070 (p0) cc_final: 0.8777 (p0)
REVERT: A  236 GLU cc_start: 0.9575 (pm20) cc_final: 0.9344 (pm20)
REVERT: A  248 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8011 (tp30)
REVERT: A  257 ASP cc_start: 0.9006 (p0) cc_final: 0.8485 (p0)
REVERT: B   91 LYS cc_start: 0.9518 (mmmm) cc_final: 0.9314 (mmmm)
REVERT: B  110 MET cc_start: 0.8692 (ptp) cc_final: 0.8470 (ptt)
REVERT: B  114 GLU cc_start: 0.7870 (pt0) cc_final: 0.7645 (pt0)
REVERT: B  135 LEU cc_start: 0.9616 (mm) cc_final: 0.9378 (tp)
REVERT: B  136 LYS cc_start: 0.8687 (mtmm) cc_final: 0.8180 (ptpp)
REVERT: B  150 HIS cc_start: 0.6045 (OUTLIER) cc_final: 0.5701 (m-70)
REVERT: B  218 GLN cc_start: 0.8362 (tt0) cc_final: 0.7848 (tm-30)
REVERT: B  236 GLU cc_start: 0.9518 (pm20) cc_final: 0.9265 (pm20)
REVERT: B  257 ASP cc_start: 0.9086 (m-30) cc_final: 0.8523 (p0)
REVERT: B  283 ARG cc_start: 0.8863 (mtm-85) cc_final: 0.8399 (ptp-110)
REVERT: B  305 ASN cc_start: 0.8553 (t0) cc_final: 0.7979 (p0)
  outliers start: 10
  outliers final: 3
  residues processed: 107
  average time/residue: 0.6605
  time to fit residues: 73.0800
Evaluate side-chains
  80 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain B residue   88 ARG
Chi-restraints excluded: chain B residue  150 HIS
Chi-restraints excluded: chain B residue  222 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 26 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 48 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 41 optimal weight:    6.9990
   chunk 49 optimal weight:   30.0000
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
B  42 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.072931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.058559 restraints weight = 12890.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 4.27
r_work: 0.2923 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.4401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5104  Z= 0.132
  Angle     :  0.610   7.552   6912  Z= 0.323
  Chirality :  0.046   0.158    758
  Planarity :  0.004   0.030    918
  Dihedral  :  4.569  20.505    688
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.90 %
    Favored  : 85.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.34), residues: 612
  helix:  1.16 (0.39), residues: 184
  sheet: -2.27 (0.75), residues: 44
  loop : -0.13 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 210 
 TYR   0.009   0.001   TYR A 216 
 PHE   0.013   0.001   PHE B  74 
 TRP   0.004   0.001   TRP A  46 
 HIS   0.014   0.002   HIS B 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 5096)
  covalent geometry    : angle       0.60240 ( 6906)
  hydrogen bonds       : bond        0.03932 (  178)
  hydrogen bonds       : angle       5.77208 (  462)
  metal coordination   : bond        0.00722 (    8)
  metal coordination   : angle       3.22549 (    6)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ASP cc_start: 0.8571 (t0) cc_final: 0.8301 (t0)
REVERT: A   62 MET cc_start: 0.8789 (mtm) cc_final: 0.8159 (mmm)
REVERT: A  110 MET cc_start: 0.8714 (ptp) cc_final: 0.6858 (ptt)
REVERT: A  114 GLU cc_start: 0.8167 (tt0) cc_final: 0.7816 (tt0)
REVERT: A  184 ASN cc_start: 0.8497 (m-40) cc_final: 0.8057 (t0)
REVERT: A  218 GLN cc_start: 0.8098 (tt0) cc_final: 0.7171 (tm130)
REVERT: A  235 ASP cc_start: 0.9101 (p0) cc_final: 0.8808 (p0)
REVERT: A  236 GLU cc_start: 0.9509 (pm20) cc_final: 0.9280 (pm20)
REVERT: A  248 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7861 (tp30)
REVERT: A  283 ARG cc_start: 0.8894 (ttp-110) cc_final: 0.8385 (ptp-110)
REVERT: B   59 MET cc_start: 0.9234 (mtt) cc_final: 0.8979 (mpt)
REVERT: B   70 ASP cc_start: 0.8702 (t0) cc_final: 0.8203 (p0)
REVERT: B   88 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7904 (mpt-90)
REVERT: B   91 LYS cc_start: 0.9507 (mmmm) cc_final: 0.9268 (mmmm)
REVERT: B  110 MET cc_start: 0.8703 (ptp) cc_final: 0.7970 (ptt)
REVERT: B  114 GLU cc_start: 0.8013 (pt0) cc_final: 0.7523 (pt0)
REVERT: B  135 LEU cc_start: 0.9540 (mm) cc_final: 0.9248 (tt)
REVERT: B  218 GLN cc_start: 0.8270 (tt0) cc_final: 0.7804 (tm-30)
REVERT: B  236 GLU cc_start: 0.9530 (pm20) cc_final: 0.9260 (pm20)
REVERT: B  257 ASP cc_start: 0.8966 (m-30) cc_final: 0.8494 (p0)
REVERT: B  290 GLU cc_start: 0.8759 (pm20) cc_final: 0.8493 (pm20)
REVERT: B  305 ASN cc_start: 0.8525 (t0) cc_final: 0.8111 (p0)
  outliers start: 9
  outliers final: 1
  residues processed: 94
  average time/residue: 0.6030
  time to fit residues: 58.8039
Evaluate side-chains
  72 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain B residue   88 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 23 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    8.9990
   chunk 19 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   chunk 9 optimal weight:    6.9990
   chunk 42 optimal weight:    0.8980
   chunk 57 optimal weight:    9.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
B  42 HIS
** B 195 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 = 0.3333 r_free = 0.3333 target = 0.071056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.056545 restraints weight = 12820.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 4.26
r_work: 0.2890 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.4689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5104  Z= 0.167
  Angle     :  0.603   7.290   6912  Z= 0.315
  Chirality :  0.046   0.159    758
  Planarity :  0.004   0.030    918
  Dihedral  :  4.466  18.455    688
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.70 %
    Favored  : 83.87 %
  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 (0.34), residues: 612
  helix:  0.88 (0.38), residues: 196
  sheet: -2.35 (0.87), residues: 36
  loop : -0.23 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  92 
 TYR   0.008   0.001   TYR A 216 
 PHE   0.020   0.002   PHE A 226 
 TRP   0.002   0.001   TRP B  46 
 HIS   0.006   0.002   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 5096)
  covalent geometry    : angle       0.59671 ( 6906)
  hydrogen bonds       : bond        0.03792 (  178)
  hydrogen bonds       : angle       5.74686 (  462)
  metal coordination   : bond        0.01551 (    8)
  metal coordination   : angle       2.92391 (    6)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ASP cc_start: 0.8535 (t0) cc_final: 0.8255 (t0)
REVERT: A  110 MET cc_start: 0.8749 (ptp) cc_final: 0.8302 (ptt)
REVERT: A  184 ASN cc_start: 0.8626 (m-40) cc_final: 0.8207 (t0)
REVERT: A  235 ASP cc_start: 0.9090 (p0) cc_final: 0.8739 (p0)
REVERT: A  236 GLU cc_start: 0.9522 (pm20) cc_final: 0.9281 (pm20)
REVERT: A  248 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7971 (tp30)
REVERT: A  318 ARG cc_start: 0.9385 (OUTLIER) cc_final: 0.8682 (mtp85)
REVERT: B   70 ASP cc_start: 0.8658 (t0) cc_final: 0.8172 (p0)
REVERT: B   74 PHE cc_start: 0.7920 (t80) cc_final: 0.7681 (t80)
REVERT: B  114 GLU cc_start: 0.8032 (pt0) cc_final: 0.7800 (pt0)
REVERT: B  218 GLN cc_start: 0.8352 (tt0) cc_final: 0.7987 (tm-30)
REVERT: B  236 GLU cc_start: 0.9501 (pm20) cc_final: 0.9246 (pm20)
REVERT: B  253 ILE cc_start: 0.8975 (mm) cc_final: 0.8603 (pp)
  outliers start: 8
  outliers final: 4
  residues processed: 81
  average time/residue: 0.7231
  time to fit residues: 60.3854
Evaluate side-chains
  70 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  318 ARG
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   88 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 52 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 46 optimal weight:    9.9990
   chunk 44 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
B 305 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.071519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.057042 restraints weight = 12970.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 4.26
r_work: 0.2891 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.4964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5104  Z= 0.160
  Angle     :  0.621   6.760   6912  Z= 0.323
  Chirality :  0.046   0.154    758
  Planarity :  0.004   0.036    918
  Dihedral  :  4.414  17.695    688
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.59 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.34), residues: 612
  helix:  0.80 (0.38), residues: 196
  sheet: -2.38 (0.85), residues: 36
  loop : -0.29 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 279 
 TYR   0.010   0.001   TYR B  32 
 PHE   0.014   0.001   PHE A 226 
 TRP   0.002   0.001   TRP B  46 
 HIS   0.004   0.001   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 5096)
  covalent geometry    : angle       0.61602 ( 6906)
  hydrogen bonds       : bond        0.03718 (  178)
  hydrogen bonds       : angle       5.68410 (  462)
  metal coordination   : bond        0.01363 (    8)
  metal coordination   : angle       2.69673 (    6)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ASP cc_start: 0.8533 (t0) cc_final: 0.8247 (t0)
REVERT: A  110 MET cc_start: 0.8841 (ptp) cc_final: 0.7838 (ptt)
REVERT: A  114 GLU cc_start: 0.8543 (tt0) cc_final: 0.8194 (tt0)
REVERT: A  184 ASN cc_start: 0.8654 (m-40) cc_final: 0.8233 (t0)
REVERT: A  218 GLN cc_start: 0.8224 (tt0) cc_final: 0.7339 (tm130)
REVERT: A  235 ASP cc_start: 0.9101 (p0) cc_final: 0.8729 (p0)
REVERT: A  236 GLU cc_start: 0.9537 (pm20) cc_final: 0.9315 (pm20)
REVERT: A  248 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7780 (tp30)
REVERT: A  318 ARG cc_start: 0.9432 (OUTLIER) cc_final: 0.8616 (mtp85)
REVERT: B   59 MET cc_start: 0.9234 (mtt) cc_final: 0.8957 (mpt)
REVERT: B   70 ASP cc_start: 0.8702 (t0) cc_final: 0.8233 (p0)
REVERT: B   74 PHE cc_start: 0.8014 (t80) cc_final: 0.7661 (t80)
REVERT: B   75 LYS cc_start: 0.8740 (mttm) cc_final: 0.8463 (mttt)
REVERT: B   82 LEU cc_start: 0.9305 (mt) cc_final: 0.8970 (mm)
REVERT: B  114 GLU cc_start: 0.8293 (pt0) cc_final: 0.7779 (pt0)
REVERT: B  135 LEU cc_start: 0.9561 (mm) cc_final: 0.9089 (pp)
REVERT: B  218 GLN cc_start: 0.8322 (tt0) cc_final: 0.7899 (tm-30)
REVERT: B  236 GLU cc_start: 0.9522 (pm20) cc_final: 0.9239 (pm20)
REVERT: B  253 ILE cc_start: 0.8995 (mm) cc_final: 0.8583 (pp)
REVERT: B  283 ARG cc_start: 0.9023 (mtm-85) cc_final: 0.8780 (mtm-85)
  outliers start: 10
  outliers final: 3
  residues processed: 87
  average time/residue: 0.7316
  time to fit residues: 65.6701
Evaluate side-chains
  73 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  318 ARG
Chi-restraints excluded: chain B residue   81 HIS
Chi-restraints excluded: chain B residue   88 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 56 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 2 optimal weight:   10.0000
   chunk 1 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
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 = 0.3339 r_free = 0.3339 target = 0.071883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.057366 restraints weight = 13125.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 4.31
r_work: 0.2897 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.5105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5104  Z= 0.143
  Angle     :  0.636   7.235   6912  Z= 0.327
  Chirality :  0.046   0.142    758
  Planarity :  0.004   0.043    918
  Dihedral  :  4.357  16.989    688
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 16.31 %
    Favored  : 82.08 %
  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: -0.18 (0.34), residues: 612
  helix:  0.75 (0.39), residues: 196
  sheet: -2.54 (0.83), residues: 36
  loop : -0.27 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 279 
 TYR   0.010   0.001   TYR B  32 
 PHE   0.010   0.001   PHE A 226 
 TRP   0.003   0.001   TRP A  46 
 HIS   0.003   0.001   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 5096)
  covalent geometry    : angle       0.63250 ( 6906)
  hydrogen bonds       : bond        0.03576 (  178)
  hydrogen bonds       : angle       5.56057 (  462)
  metal coordination   : bond        0.01008 (    8)
  metal coordination   : angle       2.31728 (    6)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ASP cc_start: 0.8618 (t0) cc_final: 0.8330 (t0)
REVERT: A  110 MET cc_start: 0.8834 (ptp) cc_final: 0.7666 (ptt)
REVERT: A  114 GLU cc_start: 0.8398 (tt0) cc_final: 0.8124 (tt0)
REVERT: A  184 ASN cc_start: 0.8657 (m-40) cc_final: 0.8243 (t0)
REVERT: A  235 ASP cc_start: 0.9067 (p0) cc_final: 0.8751 (p0)
REVERT: A  248 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7788 (tp30)
REVERT: A  318 ARG cc_start: 0.9453 (OUTLIER) cc_final: 0.8678 (mtp85)
REVERT: B   59 MET cc_start: 0.9210 (mtt) cc_final: 0.8963 (mpt)
REVERT: B   70 ASP cc_start: 0.8676 (t0) cc_final: 0.8148 (p0)
REVERT: B   74 PHE cc_start: 0.7997 (t80) cc_final: 0.7684 (t80)
REVERT: B   75 LYS cc_start: 0.8716 (mttm) cc_final: 0.8446 (mtmt)
REVERT: B   82 LEU cc_start: 0.9120 (mt) cc_final: 0.8858 (mm)
REVERT: B  114 GLU cc_start: 0.8238 (pt0) cc_final: 0.7634 (pt0)
REVERT: B  135 LEU cc_start: 0.9506 (mm) cc_final: 0.9237 (tt)
REVERT: B  215 GLU cc_start: 0.8362 (mp0) cc_final: 0.7960 (mp0)
REVERT: B  218 GLN cc_start: 0.8296 (tt0) cc_final: 0.7888 (tm-30)
REVERT: B  236 GLU cc_start: 0.9523 (pm20) cc_final: 0.9229 (pm20)
REVERT: B  253 ILE cc_start: 0.9011 (mm) cc_final: 0.8578 (pp)
REVERT: B  310 PHE cc_start: 0.9406 (t80) cc_final: 0.9142 (t80)
  outliers start: 9
  outliers final: 3
  residues processed: 86
  average time/residue: 0.6893
  time to fit residues: 61.2054
Evaluate side-chains
  76 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  318 ARG
Chi-restraints excluded: chain B residue   88 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 58 optimal weight:    8.9990
   chunk 27 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 14 optimal weight:    7.9990
   overall best weight:    4.3588

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

Flipped N/Q/H residues before XYZ refinement:
B 150 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.069710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.055404 restraints weight = 13108.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 4.25
r_work: 0.2850 rms_B_bonded: 4.64 restraints_weight: 0.5000
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.5297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   5104  Z= 0.220
  Angle     :  0.702  10.868   6912  Z= 0.360
  Chirality :  0.047   0.173    758
  Planarity :  0.005   0.045    918
  Dihedral  :  4.589  17.941    688
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 16.85 %
    Favored  : 81.72 %
  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: -0.49 (0.34), residues: 612
  helix:  0.26 (0.37), residues: 208
  sheet: -3.03 (0.77), residues: 36
  loop : -0.30 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 279 
 TYR   0.024   0.002   TYR B  32 
 PHE   0.013   0.002   PHE B 315 
 TRP   0.003   0.001   TRP B  46 
 HIS   0.005   0.002   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 5096)
  covalent geometry    : angle       0.69618 ( 6906)
  hydrogen bonds       : bond        0.03861 (  178)
  hydrogen bonds       : angle       5.68812 (  462)
  metal coordination   : bond        0.02462 (    8)
  metal coordination   : angle       3.23853 (    6)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ASP cc_start: 0.8792 (t0) cc_final: 0.8480 (t0)
REVERT: A   87 GLU cc_start: 0.8972 (mp0) cc_final: 0.8394 (mp0)
REVERT: A  102 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8874 (pm20)
REVERT: A  110 MET cc_start: 0.8836 (ptp) cc_final: 0.7590 (ptt)
REVERT: A  114 GLU cc_start: 0.8427 (tt0) cc_final: 0.8179 (tt0)
REVERT: A  184 ASN cc_start: 0.8768 (m-40) cc_final: 0.8369 (m-40)
REVERT: A  235 ASP cc_start: 0.9117 (p0) cc_final: 0.8824 (p0)
REVERT: A  236 GLU cc_start: 0.9366 (pm20) cc_final: 0.9036 (pm20)
REVERT: A  248 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7835 (tp30)
REVERT: A  318 ARG cc_start: 0.9433 (OUTLIER) cc_final: 0.8972 (mtp85)
REVERT: B   59 MET cc_start: 0.9311 (mtt) cc_final: 0.8991 (mpt)
REVERT: B   70 ASP cc_start: 0.8679 (t0) cc_final: 0.8180 (p0)
REVERT: B   75 LYS cc_start: 0.8700 (mttm) cc_final: 0.8457 (mttt)
REVERT: B  114 GLU cc_start: 0.8203 (pt0) cc_final: 0.7636 (pt0)
REVERT: B  215 GLU cc_start: 0.8294 (mp0) cc_final: 0.7689 (mp0)
REVERT: B  218 GLN cc_start: 0.8311 (tt0) cc_final: 0.7940 (tm-30)
REVERT: B  236 GLU cc_start: 0.9535 (pm20) cc_final: 0.9300 (pm20)
REVERT: B  253 ILE cc_start: 0.9074 (mm) cc_final: 0.8684 (pp)
  outliers start: 8
  outliers final: 3
  residues processed: 81
  average time/residue: 0.8153
  time to fit residues: 67.9738
Evaluate side-chains
  71 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 GLN
Chi-restraints excluded: chain A residue  174 ARG
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  318 ARG
Chi-restraints excluded: chain B residue   88 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 54 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 55 optimal weight:    8.9990
   chunk 41 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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 = 0.3342 r_free = 0.3342 target = 0.071950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.057369 restraints weight = 12948.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 4.27
r_work: 0.2903 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.5442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5104  Z= 0.131
  Angle     :  0.679  10.651   6912  Z= 0.344
  Chirality :  0.046   0.148    758
  Planarity :  0.004   0.056    918
  Dihedral  :  4.347  16.515    688
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 17.74 %
    Favored  : 81.00 %
  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: -0.29 (0.34), residues: 612
  helix:  0.78 (0.39), residues: 196
  sheet: -3.26 (0.72), residues: 36
  loop : -0.35 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 279 
 TYR   0.008   0.001   TYR A 153 
 PHE   0.009   0.001   PHE A  74 
 TRP   0.005   0.001   TRP A  46 
 HIS   0.004   0.001   HIS B 119 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 5096)
  covalent geometry    : angle       0.67650 ( 6906)
  hydrogen bonds       : bond        0.03462 (  178)
  hydrogen bonds       : angle       5.51633 (  462)
  metal coordination   : bond        0.00684 (    8)
  metal coordination   : angle       1.98242 (    6)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ASP cc_start: 0.8747 (t0) cc_final: 0.8438 (t0)
REVERT: A   87 GLU cc_start: 0.8936 (mp0) cc_final: 0.8307 (mp0)
REVERT: A  110 MET cc_start: 0.8814 (ptp) cc_final: 0.7295 (ptt)
REVERT: A  114 GLU cc_start: 0.8430 (tt0) cc_final: 0.8141 (tt0)
REVERT: A  184 ASN cc_start: 0.8681 (m-40) cc_final: 0.8256 (t0)
REVERT: A  235 ASP cc_start: 0.9070 (p0) cc_final: 0.8788 (p0)
REVERT: A  236 GLU cc_start: 0.9351 (pm20) cc_final: 0.8985 (pm20)
REVERT: A  248 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7637 (tp30)
REVERT: B   59 MET cc_start: 0.9211 (mtt) cc_final: 0.9006 (mpt)
REVERT: B   70 ASP cc_start: 0.8607 (t0) cc_final: 0.8238 (p0)
REVERT: B  114 GLU cc_start: 0.8254 (pt0) cc_final: 0.7647 (pt0)
REVERT: B  136 LYS cc_start: 0.8634 (mtmm) cc_final: 0.8288 (ptpp)
REVERT: B  194 ASP cc_start: 0.9266 (m-30) cc_final: 0.8981 (m-30)
REVERT: B  215 GLU cc_start: 0.8334 (mp0) cc_final: 0.7924 (mp0)
REVERT: B  218 GLN cc_start: 0.8264 (tt0) cc_final: 0.7818 (tm-30)
REVERT: B  236 GLU cc_start: 0.9499 (pm20) cc_final: 0.9213 (pm20)
REVERT: B  253 ILE cc_start: 0.9031 (mm) cc_final: 0.8539 (pp)
REVERT: B  259 MET cc_start: 0.6981 (mmm) cc_final: 0.6658 (mmp)
REVERT: B  310 PHE cc_start: 0.9441 (t80) cc_final: 0.9196 (t80)
REVERT: B  316 ILE cc_start: 0.9455 (mt) cc_final: 0.9224 (mp)
  outliers start: 7
  outliers final: 4
  residues processed: 82
  average time/residue: 0.7420
  time to fit residues: 62.8071
Evaluate side-chains
  73 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain B residue   81 HIS
Chi-restraints excluded: chain B residue   88 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 27 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 24 optimal weight:    5.9990
   chunk 52 optimal weight:    9.9990
   chunk 25 optimal weight:    6.9990
   chunk 51 optimal weight:    8.9990
   chunk 10 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 59 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   overall best weight:    6.7990

-------------------------------------------------------------------------------
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 = 0.3276 r_free = 0.3276 target = 0.068842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.054379 restraints weight = 13344.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 4.25
r_work: 0.2823 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.5558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.090   5104  Z= 0.317
  Angle     :  0.785   9.537   6912  Z= 0.403
  Chirality :  0.049   0.175    758
  Planarity :  0.006   0.053    918
  Dihedral  :  4.938  20.797    688
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 18.64 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.88 (0.34), residues: 612
  helix: -0.01 (0.36), residues: 208
  sheet: -3.62 (0.65), residues: 44
  loop : -0.44 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 279 
 TYR   0.021   0.002   TYR B  32 
 PHE   0.018   0.002   PHE A 315 
 TRP   0.010   0.002   TRP B  46 
 HIS   0.006   0.002   HIS B  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00710 ( 5096)
  covalent geometry    : angle       0.77619 ( 6906)
  hydrogen bonds       : bond        0.04118 (  178)
  hydrogen bonds       : angle       5.89876 (  462)
  metal coordination   : bond        0.03755 (    8)
  metal coordination   : angle       4.10602 (    6)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ASP cc_start: 0.8870 (t0) cc_final: 0.8527 (t0)
REVERT: A   87 GLU cc_start: 0.9032 (mp0) cc_final: 0.8459 (mp0)
REVERT: A  110 MET cc_start: 0.8799 (ptp) cc_final: 0.8511 (ptt)
REVERT: A  184 ASN cc_start: 0.8784 (m-40) cc_final: 0.8411 (m-40)
REVERT: A  235 ASP cc_start: 0.9077 (p0) cc_final: 0.8742 (p0)
REVERT: A  236 GLU cc_start: 0.9333 (pm20) cc_final: 0.9060 (pm20)
REVERT: A  248 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7987 (tp30)
REVERT: B   70 ASP cc_start: 0.8670 (t0) cc_final: 0.8179 (p0)
REVERT: B   86 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.9091 (mtmm)
REVERT: B  114 GLU cc_start: 0.8255 (pt0) cc_final: 0.7698 (pt0)
REVERT: B  136 LYS cc_start: 0.8833 (mtmm) cc_final: 0.7920 (ptpp)
REVERT: B  215 GLU cc_start: 0.8395 (mp0) cc_final: 0.7784 (mp0)
REVERT: B  218 GLN cc_start: 0.8337 (tt0) cc_final: 0.8014 (tm-30)
REVERT: B  236 GLU cc_start: 0.9538 (pm20) cc_final: 0.9330 (pm20)
REVERT: B  253 ILE cc_start: 0.9176 (mm) cc_final: 0.8708 (pp)
REVERT: B  283 ARG cc_start: 0.9011 (mtm-85) cc_final: 0.8758 (mtm110)
  outliers start: 7
  outliers final: 1
  residues processed: 74
  average time/residue: 0.7929
  time to fit residues: 60.4248
Evaluate side-chains
  69 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain B residue   86 LYS
Chi-restraints excluded: chain B residue   88 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 1 optimal weight:    0.0570
   chunk 19 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 39 optimal weight:    9.9990
   chunk 0 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    1.2104

-------------------------------------------------------------------------------
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 = 0.3354 r_free = 0.3354 target = 0.072897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.058267 restraints weight = 12852.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 4.29
r_work: 0.2910 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.5709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5104  Z= 0.137
  Angle     :  0.734  11.908   6912  Z= 0.372
  Chirality :  0.046   0.146    758
  Planarity :  0.005   0.066    918
  Dihedral  :  4.609  16.566    688
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 20.43 %
    Favored  : 79.21 %
  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: -0.33 (0.34), residues: 612
  helix:  0.83 (0.39), residues: 184
  sheet: -3.65 (0.70), residues: 36
  loop : -0.34 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 210 
 TYR   0.008   0.001   TYR A 153 
 PHE   0.012   0.001   PHE A  74 
 TRP   0.008   0.002   TRP B  46 
 HIS   0.007   0.002   HIS A  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 5096)
  covalent geometry    : angle       0.73220 ( 6906)
  hydrogen bonds       : bond        0.03483 (  178)
  hydrogen bonds       : angle       5.69428 (  462)
  metal coordination   : bond        0.00509 (    8)
  metal coordination   : angle       1.92179 (    6)

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

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

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1224 Ramachandran restraints generated.
    612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ASP cc_start: 0.8745 (t0) cc_final: 0.8417 (t0)
REVERT: A   87 GLU cc_start: 0.9016 (mp0) cc_final: 0.8407 (mp0)
REVERT: A  110 MET cc_start: 0.8723 (ptp) cc_final: 0.8019 (ptt)
REVERT: A  114 GLU cc_start: 0.8068 (tt0) cc_final: 0.7851 (tt0)
REVERT: A  184 ASN cc_start: 0.8777 (m-40) cc_final: 0.8370 (m-40)
REVERT: A  218 GLN cc_start: 0.8220 (tt0) cc_final: 0.7372 (tm130)
REVERT: A  235 ASP cc_start: 0.9086 (p0) cc_final: 0.8788 (p0)
REVERT: A  236 GLU cc_start: 0.9386 (pm20) cc_final: 0.9027 (pm20)
REVERT: A  248 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7661 (tp30)
REVERT: A  283 ARG cc_start: 0.8876 (ptt-90) cc_final: 0.8569 (pmm-80)
REVERT: B   59 MET cc_start: 0.9107 (mtt) cc_final: 0.8877 (mpt)
REVERT: B   70 ASP cc_start: 0.8488 (t0) cc_final: 0.8141 (p0)
REVERT: B  114 GLU cc_start: 0.8368 (pt0) cc_final: 0.7721 (pt0)
REVERT: B  136 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8515 (ptpp)
REVERT: B  215 GLU cc_start: 0.8293 (mp0) cc_final: 0.7747 (mp0)
REVERT: B  218 GLN cc_start: 0.8279 (tt0) cc_final: 0.7915 (tm-30)
REVERT: B  236 GLU cc_start: 0.9501 (pm20) cc_final: 0.9216 (pm20)
REVERT: B  253 ILE cc_start: 0.9062 (mm) cc_final: 0.8529 (pp)
REVERT: B  259 MET cc_start: 0.7070 (mmm) cc_final: 0.6745 (mmp)
  outliers start: 2
  outliers final: 2
  residues processed: 73
  average time/residue: 0.8073
  time to fit residues: 60.7246
Evaluate side-chains
  69 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 GLU
Chi-restraints excluded: chain B residue   81 HIS
Chi-restraints excluded: chain B residue   88 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 30 optimal weight:   10.0000
   chunk 49 optimal weight:   20.0000
   chunk 39 optimal weight:    2.9990
   chunk 12 optimal weight:    8.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 102 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.071836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.057391 restraints weight = 13482.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3022 rms_B_bonded: 4.37
r_work: 0.2877 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.5773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5104  Z= 0.157
  Angle     :  0.731  11.515   6912  Z= 0.370
  Chirality :  0.046   0.149    758
  Planarity :  0.005   0.052    918
  Dihedral  :  4.611  19.294    688
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 20.61 %
    Favored  : 78.49 %
  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: -0.48 (0.34), residues: 612
  helix:  0.54 (0.38), residues: 196
  sheet: -3.55 (0.71), residues: 36
  loop : -0.38 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 283 
 TYR   0.028   0.001   TYR B  32 
 PHE   0.011   0.001   PHE A  74 
 TRP   0.003   0.001   TRP A  46 
 HIS   0.007   0.002   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 5096)
  covalent geometry    : angle       0.72878 ( 6906)
  hydrogen bonds       : bond        0.03611 (  178)
  hydrogen bonds       : angle       5.68662 (  462)
  metal coordination   : bond        0.01157 (    8)
  metal coordination   : angle       2.22798 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2010.77 seconds
wall clock time: 35 minutes 9.76 seconds (2109.76 seconds total)