Starting phenix.real_space_refine
on Sat Apr  4 22:12:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w03_65490/04_2026/9w03_65490_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w03_65490/04_2026/9w03_65490.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w03_65490/04_2026/9w03_65490_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w03_65490/04_2026/9w03_65490_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w03_65490/04_2026/9w03_65490.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w03_65490/04_2026/9w03_65490.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
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      36      5.49       5
     S      24      5.16       5
     C    2736      2.51       5
     N     855      2.21       5
     O     945      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4596
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 1972
          Classifications: {'peptide': 246}
          Link IDs: {'PTRANS': 8, 'TRANS': 237}
    Chain: "B"
      Number of atoms: 1850
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1850
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 8, 'TRANS': 221}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 774
          Classifications: {'DNA': 1, 'RNA': 36}
          Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 7, 'rna3p_pur': 8, 'rna3p_pyr': 7}
          Link IDs: {'rna2p': 21, 'rna3p': 15}
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'  A:plan': 1, '  A:plan2': 1}
          Unresolved non-hydrogen planarities: 13
  Time building chain proxies: 1.17, per 1000 atoms: 0.25
  Number of scatterers: 4596
  At special positions: 0
  Unit cell: (67.425, 65.25, 109.475, 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      24     16.00
     P      36     15.00
     O     945      8.00
     N     855      7.00
     C    2736      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: 0.44
  Conformation dependent library (CDL) restraints added in 274.9 milliseconds
  

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  896

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 2 sheets defined
      71.2% alpha, 2.5% beta
      4 base pairs and 7 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 98
      removed outlier: 3.672A  pdb=" N   LYS A  87 " --> pdb=" O   LYS A  83 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLN A  98 " --> pdb=" O   ALA A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 133
      removed outlier: 4.048A  pdb=" N   LEU A 110 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 145
    Processing helix  chain 'A' and resid 150 through 160
    Processing helix  chain 'A' and resid 162 through 166
    Processing helix  chain 'A' and resid 170 through 177
      removed outlier: 3.619A  pdb=" N   ALA A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ILE A 176 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 183
      No H-bonds generated for 'chain 'A' and resid 181 through 183'
    Processing helix  chain 'A' and resid 184 through 190
      removed outlier: 4.106A  pdb=" N   GLY A 189 " --> pdb=" O   ARG A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 212
      removed outlier: 3.644A  pdb=" N   LYS A 211 " --> pdb=" O   ASN A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 231
      removed outlier: 3.606A  pdb=" N   TYR A 221 " --> pdb=" O   TYR A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 242
      No H-bonds generated for 'chain 'A' and resid 240 through 242'
    Processing helix  chain 'A' and resid 253 through 281
      removed outlier: 3.877A  pdb=" N   ARG A 257 " --> pdb=" O   LYS A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 294
    Processing helix  chain 'B' and resid 67 through 97
    Processing helix  chain 'B' and resid 104 through 134
      removed outlier: 3.717A  pdb=" N   PHE B 109 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 146
    Processing helix  chain 'B' and resid 152 through 157
      removed outlier: 3.662A  pdb=" N   LEU B 157 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 166
    Processing helix  chain 'B' and resid 170 through 177
      removed outlier: 3.551A  pdb=" N   ALA B 174 " --> pdb=" O   SER B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 185
    Processing helix  chain 'B' and resid 195 through 210
      removed outlier: 3.513A  pdb=" N   MET B 201 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 230
      removed outlier: 4.258A  pdb=" N   VAL B 220 " --> pdb=" O   PRO B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 282
      removed outlier: 3.543A  pdb=" N   ARG B 257 " --> pdb=" O   LYS B 253 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 306
    Processing sheet with id=AA1, first strand: chain 'A' and resid 237 through 239
    Processing sheet with id=AA2, first strand: chain 'B' and resid 234 through 238

    242 hydrogen bonds defined for protein.
    696 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      9 hydrogen bonds
      10 hydrogen bond angles
      0 basepair planarities
      4 basepair parallelities
      7 stacking parallelities
  Total time for adding SS restraints: 0.54

  Time building geometry restraints manager: 0.58 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1286
        1.33 -     1.45: 945
        1.45 -     1.57: 2418
        1.57 -     1.69: 72
        1.69 -     1.81: 44
  Bond restraints: 4765
  Sorted by residual:
  bond pdb=" P     A C  37 "
       pdb=" OP2   A C  37 "
    ideal  model  delta    sigma   weight residual
    1.480  1.515 -0.035 2.00e-02 2.50e+03 3.00e+00
  bond pdb=" N   ARG A  64 "
       pdb=" CA  ARG A  64 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.90e+00
  bond pdb=" N   ASP B  65 "
       pdb=" CA  ASP B  65 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.79e+00
  bond pdb=" P     A C  37 "
       pdb=" OP1   A C  37 "
    ideal  model  delta    sigma   weight residual
    1.480  1.513 -0.033 2.00e-02 2.50e+03 2.69e+00
  bond pdb=" P     G C  36 "
       pdb=" OP1   G C  36 "
    ideal  model  delta    sigma   weight residual
    1.485  1.517 -0.032 2.00e-02 2.50e+03 2.53e+00
  ... (remaining 4760 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.24: 6264
        1.24 -     2.48: 261
        2.48 -     3.72: 61
        3.72 -     4.96: 16
        4.96 -     6.20: 5
  Bond angle restraints: 6607
  Sorted by residual:
  angle pdb=" CA  GLN A  66 "
        pdb=" CB  GLN A  66 "
        pdb=" CG  GLN A  66 "
      ideal   model   delta    sigma   weight residual
     114.10  120.30   -6.20 2.00e+00 2.50e-01 9.60e+00
  angle pdb=" N   TRP A 249 "
        pdb=" CA  TRP A 249 "
        pdb=" C   TRP A 249 "
      ideal   model   delta    sigma   weight residual
     113.43  110.19    3.24 1.26e+00 6.30e-01 6.62e+00
  angle pdb=" C   ALA A 248 "
        pdb=" CA  ALA A 248 "
        pdb=" CB  ALA A 248 "
      ideal   model   delta    sigma   weight residual
     110.42  115.47   -5.05 1.99e+00 2.53e-01 6.44e+00
  angle pdb=" N   LEU B 283 "
        pdb=" CA  LEU B 283 "
        pdb=" C   LEU B 283 "
      ideal   model   delta    sigma   weight residual
     112.72  109.53    3.19 1.28e+00 6.10e-01 6.21e+00
  angle pdb=" C4'   G C  36 "
        pdb=" O4'   G C  36 "
        pdb=" C1'   G C  36 "
      ideal   model   delta    sigma   weight residual
     109.70  107.33    2.37 1.00e+00 1.00e+00 5.59e+00
  ... (remaining 6602 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.34: 2747
       35.34 -    70.68: 143
       70.68 -   106.01: 18
      106.01 -   141.35: 5
      141.35 -   176.69: 1
  Dihedral angle restraints: 2914
    sinusoidal: 1531
      harmonic: 1383
  Sorted by residual:
  dihedral pdb=" O4'   U C  12 "
           pdb=" C1'   U C  12 "
           pdb=" N1    U C  12 "
           pdb=" C2    U C  12 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   75.93  124.07     1      1.50e+01 4.44e-03 6.66e+01
  dihedral pdb=" O4'   A C  29 "
           pdb=" C1'   A C  29 "
           pdb=" N9    A C  29 "
           pdb=" C4    A C  29 "
      ideal   model   delta sinusoidal    sigma   weight residual
      68.00  136.23  -68.23     1      1.70e+01 3.46e-03 2.09e+01
  dihedral pdb=" C4'   G C  10 "
           pdb=" C3'   G C  10 "
           pdb=" O3'   G C  10 "
           pdb=" P     U C  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -110.00   66.69 -176.69     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 2911 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 727
       0.100 -    0.201: 16
       0.201 -    0.301: 0
       0.301 -    0.402: 0
       0.402 -    0.502: 2
  Chirality restraints: 745
  Sorted by residual:
  chirality pdb=" P     A C  37 "
            pdb=" OP1   A C  37 "
            pdb=" OP2   A C  37 "
            pdb=" O5'   A C  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.85   -0.50 2.00e-01 2.50e+01 6.31e+00
  chirality pdb=" P     G C  36 "
            pdb=" OP1   G C  36 "
            pdb=" OP2   G C  36 "
            pdb=" O5'   G C  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.91   -0.50 2.00e-01 2.50e+01 6.30e+00
  chirality pdb=" CA  VAL B 146 "
            pdb=" N   VAL B 146 "
            pdb=" C   VAL B 146 "
            pdb=" CB  VAL B 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.69e-01
  ... (remaining 742 not shown)

  Planarity restraints: 710
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 146 "   -0.041 5.00e-02 4.00e+02   6.07e-02 5.89e+00
        pdb=" N   PRO B 147 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO B 147 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 147 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 221 "    0.014 2.00e-02 2.50e+03   1.30e-02 3.40e+00
        pdb=" CG  TYR B 221 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 221 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 221 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 221 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 221 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 221 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 221 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C   2 "   -0.024 2.00e-02 2.50e+03   1.04e-02 3.23e+00
        pdb=" N9    G C   2 "    0.025 2.00e-02 2.50e+03
        pdb=" C8    G C   2 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    G C   2 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G C   2 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G C   2 "   -0.003 2.00e-02 2.50e+03
        pdb=" O6    G C   2 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    G C   2 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    G C   2 "    0.002 2.00e-02 2.50e+03
        pdb=" N2    G C   2 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G C   2 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    G C   2 "    0.001 2.00e-02 2.50e+03
  ... (remaining 707 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.42: 24
        2.42 -     3.04: 3056
        3.04 -     3.66: 7128
        3.66 -     4.28: 10214
        4.28 -     4.90: 16406
  Nonbonded interactions: 36828
  Sorted by model distance:
  nonbonded pdb=" O2'   A C  17 "
            pdb=" OP1   C C  18 "
     model   vdw
     1.800 3.040
  nonbonded pdb=" OD1 ASP A  77 "
            pdb=" OG1 THR B 106 "
     model   vdw
     2.006 3.040
  nonbonded pdb=" O   TRP A 249 "
            pdb=" OG1 THR A 252 "
     model   vdw
     2.061 3.040
  nonbonded pdb=" OG1 THR A 106 "
            pdb=" OD2 ASP B  77 "
     model   vdw
     2.103 3.040
  nonbonded pdb=" NH1 ARG B  78 "
            pdb=" OD1 ASP B 125 "
     model   vdw
     2.131 3.120
  ... (remaining 36823 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 65 through 187 or resid 194 through 287 or resid 297 throu \ 
gh 309))
  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:             1.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.500
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4765  Z= 0.183
  Angle     :  0.644   6.198   6607  Z= 0.356
  Chirality :  0.044   0.502    745
  Planarity :  0.005   0.061    710
  Dihedral  : 20.401 176.688   2018
  Min Nonbonded Distance : 1.800

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  5.98 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 16.21 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.40), residues: 468
  helix:  1.99 (0.30), residues: 288
  sheet:  None (None), residues: 0
  loop : -1.04 (0.48), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 278 
 TYR   0.031   0.002   TYR B 221 
 PHE   0.005   0.001   PHE A 109 
 TRP   0.024   0.002   TRP B 249 
 HIS   0.005   0.001   HIS B 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 4765)
  covalent geometry    : angle       0.64361 ( 6607)
  hydrogen bonds       : bond        0.16122 (  251)
  hydrogen bonds       : angle       5.53019 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 TYR cc_start: 0.7888 (t80) cc_final: 0.7118 (t80)
REVERT: A  209 MET cc_start: 0.7298 (mtm) cc_final: 0.6992 (mtm)
REVERT: A  278 ARG cc_start: 0.8002 (mmm-85) cc_final: 0.7784 (mtp85)
REVERT: B  117 SER cc_start: 0.8319 (m) cc_final: 0.8043 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1126
  time to fit residues: 13.8445
Evaluate side-chains
  103 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.1980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4303 r_free = 0.4303 target = 0.171667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.149982 restraints weight = 6955.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.4060 rms_B_bonded: 2.53
r_work: 0.3895 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4765  Z= 0.163
  Angle     :  0.679   8.757   6607  Z= 0.343
  Chirality :  0.042   0.184    745
  Planarity :  0.004   0.038    710
  Dihedral  : 21.229 167.877   1060
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  5.56 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 15.21 %
    Favored  : 81.30 %
  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 are not related in a simple way.
  whole:  1.48 (0.40), residues: 468
  helix:  2.08 (0.30), residues: 297
  sheet:  None (None), residues: 0
  loop : -1.04 (0.52), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 278 
 TYR   0.017   0.002   TYR A 221 
 PHE   0.005   0.001   PHE A 109 
 TRP   0.012   0.002   TRP B 249 
 HIS   0.004   0.001   HIS B 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4765)
  covalent geometry    : angle       0.67946 ( 6607)
  hydrogen bonds       : bond        0.05763 (  251)
  hydrogen bonds       : angle       4.55305 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.5809 (tmm) cc_final: 0.5564 (tmm)
REVERT: A   95 TYR cc_start: 0.7898 (t80) cc_final: 0.7147 (t80)
REVERT: A  279 GLU cc_start: 0.7849 (tp30) cc_final: 0.7551 (tp30)
REVERT: B   76 ASP cc_start: 0.7991 (t0) cc_final: 0.7696 (t0)
REVERT: B  137 ASP cc_start: 0.7315 (t0) cc_final: 0.7045 (t0)
  outliers start: 14
  outliers final: 7
  residues processed: 111
  average time/residue: 0.0866
  time to fit residues: 11.8246
Evaluate side-chains
  113 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain B residue   90 ASN
Chi-restraints excluded: chain B residue  159 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   chunk 28 optimal weight:    0.8980
   chunk 46 optimal weight:    0.0070
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
B  90 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.171113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.148788 restraints weight = 6938.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.4051 rms_B_bonded: 2.68
r_work: 0.3885 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4765  Z= 0.145
  Angle     :  0.622   8.598   6607  Z= 0.313
  Chirality :  0.039   0.165    745
  Planarity :  0.004   0.041    710
  Dihedral  : 21.224 169.640   1060
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.70 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 18.20 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.41), residues: 468
  helix:  2.28 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.81 (0.55), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 278 
 TYR   0.013   0.001   TYR A 221 
 PHE   0.010   0.001   PHE A 275 
 TRP   0.014   0.002   TRP B 309 
 HIS   0.004   0.001   HIS B 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4765)
  covalent geometry    : angle       0.62159 ( 6607)
  hydrogen bonds       : bond        0.05121 (  251)
  hydrogen bonds       : angle       4.21748 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.5952 (tmm) cc_final: 0.5581 (tmm)
REVERT: A   95 TYR cc_start: 0.8016 (t80) cc_final: 0.7420 (t80)
REVERT: A  119 LYS cc_start: 0.8174 (mmtp) cc_final: 0.7965 (mmtp)
REVERT: A  278 ARG cc_start: 0.7926 (mmm-85) cc_final: 0.7645 (mtp85)
REVERT: A  279 GLU cc_start: 0.7865 (tp30) cc_final: 0.7539 (tp30)
REVERT: B   91 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7489 (tm-30)
REVERT: B  126 ARG cc_start: 0.7380 (mtt90) cc_final: 0.6799 (mtm110)
REVERT: B  137 ASP cc_start: 0.7367 (t0) cc_final: 0.7083 (t0)
  outliers start: 11
  outliers final: 7
  residues processed: 112
  average time/residue: 0.0911
  time to fit residues: 12.3073
Evaluate side-chains
  113 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  159 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 32 optimal weight:    0.0040
   chunk 43 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0060
   chunk 11 optimal weight:    0.3980
   chunk 36 optimal weight:    0.1980
   chunk 10 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 39 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 41 optimal weight:    7.9990
   overall best weight:    0.2208

-------------------------------------------------------------------------------
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 = 0.4347 r_free = 0.4347 target = 0.174559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.152063 restraints weight = 6964.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.4089 rms_B_bonded: 2.66
r_work: 0.3926 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4765  Z= 0.113
  Angle     :  0.586   8.852   6607  Z= 0.291
  Chirality :  0.037   0.178    745
  Planarity :  0.004   0.042    710
  Dihedral  : 21.057 168.752   1060
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.91 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 18.20 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.18 (0.41), residues: 468
  helix:  2.59 (0.29), residues: 300
  sheet:  None (None), residues: 0
  loop : -0.74 (0.56), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 278 
 TYR   0.013   0.001   TYR A 221 
 PHE   0.009   0.001   PHE A 109 
 TRP   0.011   0.001   TRP B  67 
 HIS   0.003   0.001   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 4765)
  covalent geometry    : angle       0.58553 ( 6607)
  hydrogen bonds       : bond        0.04379 (  251)
  hydrogen bonds       : angle       3.85048 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.6049 (tmm) cc_final: 0.5642 (tmm)
REVERT: A   95 TYR cc_start: 0.7898 (t80) cc_final: 0.7307 (t80)
REVERT: A  279 GLU cc_start: 0.7759 (tp30) cc_final: 0.7403 (tp30)
REVERT: A  305 ARG cc_start: 0.8500 (mtt180) cc_final: 0.8183 (mtt90)
REVERT: B   76 ASP cc_start: 0.7999 (t0) cc_final: 0.7700 (t0)
REVERT: B  104 GLN cc_start: 0.7814 (mp10) cc_final: 0.7490 (mp10)
REVERT: B  137 ASP cc_start: 0.7084 (t0) cc_final: 0.6744 (t0)
REVERT: B  185 ARG cc_start: 0.8401 (tpp80) cc_final: 0.8142 (tpp80)
REVERT: B  219 THR cc_start: 0.7634 (m) cc_final: 0.7355 (p)
REVERT: B  266 MET cc_start: 0.7216 (mtp) cc_final: 0.6905 (mtp)
  outliers start: 12
  outliers final: 8
  residues processed: 123
  average time/residue: 0.1141
  time to fit residues: 16.3282
Evaluate side-chains
  119 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  132 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0000
   chunk 33 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 24 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 13 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.172643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.150765 restraints weight = 6893.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 2.56
r_work: 0.3904 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6944
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4765  Z= 0.140
  Angle     :  0.605   8.695   6607  Z= 0.305
  Chirality :  0.038   0.179    745
  Planarity :  0.004   0.041    710
  Dihedral  : 21.118 168.867   1060
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.49 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 19.95 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.11 (0.41), residues: 468
  helix:  2.55 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.78 (0.55), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 278 
 TYR   0.015   0.001   TYR A 221 
 PHE   0.010   0.001   PHE A 275 
 TRP   0.008   0.001   TRP B  67 
 HIS   0.004   0.001   HIS B 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 4765)
  covalent geometry    : angle       0.60546 ( 6607)
  hydrogen bonds       : bond        0.04754 (  251)
  hydrogen bonds       : angle       4.06195 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 MET cc_start: 0.6032 (tmm) cc_final: 0.5630 (tmm)
REVERT: A   95 TYR cc_start: 0.8007 (t80) cc_final: 0.7404 (t80)
REVERT: A  222 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6781 (mt-10)
REVERT: A  279 GLU cc_start: 0.7764 (tp30) cc_final: 0.7414 (tp30)
REVERT: B   76 ASP cc_start: 0.7945 (t0) cc_final: 0.7662 (t0)
REVERT: B  104 GLN cc_start: 0.7828 (mp10) cc_final: 0.7626 (mp10)
REVERT: B  126 ARG cc_start: 0.7344 (mtt90) cc_final: 0.6741 (mtm110)
REVERT: B  137 ASP cc_start: 0.7143 (t0) cc_final: 0.6872 (t0)
REVERT: B  219 THR cc_start: 0.7714 (m) cc_final: 0.7414 (p)
REVERT: B  257 ARG cc_start: 0.6962 (mtt-85) cc_final: 0.6587 (mtt90)
  outliers start: 14
  outliers final: 9
  residues processed: 122
  average time/residue: 0.1175
  time to fit residues: 16.7051
Evaluate side-chains
  124 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain B residue  108 GLN
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  159 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0020
   chunk 0 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.171906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.149789 restraints weight = 7046.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.4061 rms_B_bonded: 2.66
r_work: 0.3895 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6959
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4765  Z= 0.139
  Angle     :  0.597   8.605   6607  Z= 0.301
  Chirality :  0.038   0.181    745
  Planarity :  0.004   0.043    710
  Dihedral  : 21.133 168.203   1060
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.70 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.20 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.41), residues: 468
  helix:  2.50 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.77 (0.54), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 278 
 TYR   0.015   0.001   TYR A 221 
 PHE   0.012   0.002   PHE A 275 
 TRP   0.008   0.001   TRP B  67 
 HIS   0.003   0.001   HIS B 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4765)
  covalent geometry    : angle       0.59665 ( 6607)
  hydrogen bonds       : bond        0.04736 (  251)
  hydrogen bonds       : angle       4.01308 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 TYR cc_start: 0.8035 (t80) cc_final: 0.7453 (t80)
REVERT: A  222 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6797 (mt-10)
REVERT: A  278 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.6790 (mmm-85)
REVERT: A  279 GLU cc_start: 0.7738 (tp30) cc_final: 0.7394 (tp30)
REVERT: B   76 ASP cc_start: 0.8008 (t0) cc_final: 0.7704 (t0)
REVERT: B  104 GLN cc_start: 0.7880 (mp10) cc_final: 0.7653 (mp10)
REVERT: B  126 ARG cc_start: 0.7358 (mtt90) cc_final: 0.6988 (mtm110)
REVERT: B  137 ASP cc_start: 0.7173 (t0) cc_final: 0.6875 (t0)
REVERT: B  219 THR cc_start: 0.7719 (m) cc_final: 0.7413 (p)
  outliers start: 13
  outliers final: 9
  residues processed: 120
  average time/residue: 0.1149
  time to fit residues: 16.2034
Evaluate side-chains
  123 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain B residue  108 GLN
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  159 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0980
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.171648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.149667 restraints weight = 6910.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.4062 rms_B_bonded: 2.64
r_work: 0.3898 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6961
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4765  Z= 0.144
  Angle     :  0.605   8.551   6607  Z= 0.305
  Chirality :  0.039   0.182    745
  Planarity :  0.004   0.043    710
  Dihedral  : 21.162 167.841   1060
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.85 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 20.20 %
    Favored  : 76.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.07 (0.41), residues: 468
  helix:  2.48 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -0.72 (0.54), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 278 
 TYR   0.016   0.001   TYR A 221 
 PHE   0.015   0.002   PHE A 275 
 TRP   0.014   0.001   TRP B 309 
 HIS   0.004   0.001   HIS B 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4765)
  covalent geometry    : angle       0.60487 ( 6607)
  hydrogen bonds       : bond        0.04782 (  251)
  hydrogen bonds       : angle       4.09813 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 TYR cc_start: 0.8018 (t80) cc_final: 0.7452 (t80)
REVERT: A  222 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6806 (mt-10)
REVERT: A  279 GLU cc_start: 0.7736 (tp30) cc_final: 0.7385 (tp30)
REVERT: B   76 ASP cc_start: 0.8024 (t0) cc_final: 0.7721 (t0)
REVERT: B  104 GLN cc_start: 0.7886 (mp10) cc_final: 0.7650 (mp10)
REVERT: B  126 ARG cc_start: 0.7383 (mtt90) cc_final: 0.7010 (mtm110)
REVERT: B  137 ASP cc_start: 0.7163 (t0) cc_final: 0.6878 (t0)
REVERT: B  267 LYS cc_start: 0.7449 (mttt) cc_final: 0.7193 (mmmm)
  outliers start: 12
  outliers final: 9
  residues processed: 112
  average time/residue: 0.0847
  time to fit residues: 11.5006
Evaluate side-chains
  116 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain B residue  108 GLN
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  308 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0020
   chunk 10 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 23 optimal weight:    0.3980
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
A 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.171387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.149230 restraints weight = 7073.840|
|-----------------------------------------------------------------------------|
r_work (start): 0.4061 rms_B_bonded: 2.67
r_work: 0.3897 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6963
moved from start:          0.2855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4765  Z= 0.144
  Angle     :  0.607   8.496   6607  Z= 0.306
  Chirality :  0.039   0.184    745
  Planarity :  0.004   0.043    710
  Dihedral  : 21.163 167.413   1060
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.49 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 20.45 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.41), residues: 468
  helix:  2.38 (0.29), residues: 300
  sheet:  None (None), residues: 0
  loop : -0.66 (0.55), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 278 
 TYR   0.015   0.001   TYR A 221 
 PHE   0.015   0.002   PHE A 275 
 TRP   0.012   0.001   TRP B 309 
 HIS   0.003   0.001   HIS B 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 4765)
  covalent geometry    : angle       0.60713 ( 6607)
  hydrogen bonds       : bond        0.04786 (  251)
  hydrogen bonds       : angle       4.07153 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 TYR cc_start: 0.8023 (t80) cc_final: 0.7503 (t80)
REVERT: A  222 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6828 (mt-10)
REVERT: A  278 ARG cc_start: 0.7778 (mmm-85) cc_final: 0.6669 (mtp85)
REVERT: B   76 ASP cc_start: 0.8031 (t0) cc_final: 0.7724 (t0)
REVERT: B  104 GLN cc_start: 0.7877 (mp10) cc_final: 0.7626 (mp10)
REVERT: B  126 ARG cc_start: 0.7374 (mtt90) cc_final: 0.7001 (mtm110)
REVERT: B  137 ASP cc_start: 0.7164 (t0) cc_final: 0.6901 (t0)
REVERT: B  185 ARG cc_start: 0.8460 (tpp80) cc_final: 0.8253 (tpp80)
REVERT: B  257 ARG cc_start: 0.7014 (mtt-85) cc_final: 0.6619 (mtt90)
REVERT: B  267 LYS cc_start: 0.7425 (mttt) cc_final: 0.7168 (mmmm)
  outliers start: 15
  outliers final: 10
  residues processed: 118
  average time/residue: 0.1007
  time to fit residues: 13.9898
Evaluate side-chains
  123 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  108 GLN
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  159 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 40 optimal weight:    9.9990
   chunk 19 optimal weight:    0.0980
   chunk 24 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.172106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.150333 restraints weight = 6979.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 2.64
r_work: 0.3909 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.2951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4765  Z= 0.138
  Angle     :  0.600   8.462   6607  Z= 0.304
  Chirality :  0.039   0.185    745
  Planarity :  0.004   0.044    710
  Dihedral  : 21.140 167.091   1060
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.49 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 20.95 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.04 (0.41), residues: 468
  helix:  2.39 (0.29), residues: 300
  sheet:  None (None), residues: 0
  loop : -0.61 (0.55), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 278 
 TYR   0.015   0.001   TYR A 221 
 PHE   0.016   0.002   PHE A 275 
 TRP   0.012   0.001   TRP B 309 
 HIS   0.003   0.001   HIS B 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4765)
  covalent geometry    : angle       0.60026 ( 6607)
  hydrogen bonds       : bond        0.04692 (  251)
  hydrogen bonds       : angle       4.11697 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 TYR cc_start: 0.8020 (t80) cc_final: 0.7484 (t80)
REVERT: A  222 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6804 (mt-10)
REVERT: A  278 ARG cc_start: 0.7785 (mmm-85) cc_final: 0.7552 (mtp85)
REVERT: B   76 ASP cc_start: 0.8043 (t0) cc_final: 0.7746 (t0)
REVERT: B   86 MET cc_start: 0.6459 (tmm) cc_final: 0.6186 (tmm)
REVERT: B  104 GLN cc_start: 0.7878 (mp10) cc_final: 0.7613 (mp10)
REVERT: B  126 ARG cc_start: 0.7384 (mtt90) cc_final: 0.7018 (mtm110)
REVERT: B  137 ASP cc_start: 0.7118 (t0) cc_final: 0.6834 (t0)
  outliers start: 12
  outliers final: 9
  residues processed: 110
  average time/residue: 0.0899
  time to fit residues: 11.9447
Evaluate side-chains
  114 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain B residue  108 GLN
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  159 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 33 optimal weight:    0.4980
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 223 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.171590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.150077 restraints weight = 6973.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.4069 rms_B_bonded: 2.62
r_work: 0.3901 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6973
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4765  Z= 0.155
  Angle     :  0.619   8.409   6607  Z= 0.313
  Chirality :  0.040   0.186    745
  Planarity :  0.004   0.044    710
  Dihedral  : 21.146 166.984   1060
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.49 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 20.95 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.40), residues: 468
  helix:  2.26 (0.29), residues: 300
  sheet:  None (None), residues: 0
  loop : -0.69 (0.54), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 278 
 TYR   0.016   0.002   TYR A 221 
 PHE   0.012   0.002   PHE A 275 
 TRP   0.011   0.001   TRP B 309 
 HIS   0.004   0.001   HIS B 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 4765)
  covalent geometry    : angle       0.61891 ( 6607)
  hydrogen bonds       : bond        0.04875 (  251)
  hydrogen bonds       : angle       4.14840 (  706)

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

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

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  936 Ramachandran restraints generated.
    468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 TYR cc_start: 0.8068 (t80) cc_final: 0.7454 (t80)
REVERT: A  222 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6827 (mt-10)
REVERT: A  223 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8180 (mt0)
REVERT: A  278 ARG cc_start: 0.7790 (mmm-85) cc_final: 0.7567 (mtp85)
REVERT: A  305 ARG cc_start: 0.8659 (mtt90) cc_final: 0.8295 (mtt90)
REVERT: B   86 MET cc_start: 0.6501 (tmm) cc_final: 0.6219 (tmm)
REVERT: B  104 GLN cc_start: 0.7912 (mp10) cc_final: 0.7659 (mp10)
REVERT: B  126 ARG cc_start: 0.7414 (mtt90) cc_final: 0.7040 (mtm110)
REVERT: B  137 ASP cc_start: 0.7168 (t0) cc_final: 0.6903 (t0)
REVERT: B  267 LYS cc_start: 0.7438 (mttt) cc_final: 0.7196 (mmmm)
  outliers start: 13
  outliers final: 8
  residues processed: 114
  average time/residue: 0.1088
  time to fit residues: 14.5802
Evaluate side-chains
  118 residues out of total 401 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 MET
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  222 GLU
Chi-restraints excluded: chain A residue  223 GLN
Chi-restraints excluded: chain A residue  256 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain B residue  108 GLN
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  159 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.170787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.149165 restraints weight = 7074.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.4044 rms_B_bonded: 2.62
r_work: 0.3882 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4765  Z= 0.168
  Angle     :  0.622   8.376   6607  Z= 0.316
  Chirality :  0.040   0.186    745
  Planarity :  0.004   0.044    710
  Dihedral  : 21.183 166.964   1060
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  4.49 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 21.95 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.40), residues: 468
  helix:  2.22 (0.29), residues: 300
  sheet:  None (None), residues: 0
  loop : -0.63 (0.54), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 278 
 TYR   0.016   0.002   TYR A 221 
 PHE   0.010   0.002   PHE A 275 
 TRP   0.011   0.001   TRP B 309 
 HIS   0.004   0.001   HIS B 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 4765)
  covalent geometry    : angle       0.62228 ( 6607)
  hydrogen bonds       : bond        0.04971 (  251)
  hydrogen bonds       : angle       4.23503 (  706)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1176.93 seconds
wall clock time: 20 minutes 50.28 seconds (1250.28 seconds total)