Starting phenix.real_space_refine
on Wed Sep 17 08:15:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kqf_62503/09_2025/9kqf_62503.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kqf_62503/09_2025/9kqf_62503.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kqf_62503/09_2025/9kqf_62503.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kqf_62503/09_2025/9kqf_62503.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kqf_62503/09_2025/9kqf_62503.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kqf_62503/09_2025/9kqf_62503.cif"
  }
  resolution = 3.25
  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=   0.002 sd=   0.061
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      16      5.49       5
     S      40      5.16       5
     C    4830      2.51       5
     N    1016      2.21       5
     O    1164      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  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: 7066
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 3171
          Classifications: {'peptide': 377}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 364}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 3171
          Classifications: {'peptide': 377}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 364}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 400
          Unusual residues: {'C14': 1, 'D12': 1, 'LBN': 6, 'PSF': 2, 'T7X': 1}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 59
          Planarities with less than four sites: {'LBN:plan-3': 3}
          Unresolved non-hydrogen planarities: 11
    Chain: "B"
      Number of atoms: 324
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 324
          Unusual residues: {'C14': 1, 'D12': 1, 'LBN': 4, 'PSF': 2, 'T7X': 1}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 31
          Planarities with less than four sites: {'LBN:plan-3': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 2.04, per 1000 atoms: 0.29
  Number of scatterers: 7066
  At special positions: 0
  Unit cell: (91.785, 108.665, 71.74, 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      40     16.00
     P      16     15.00
     O    1164      8.00
     N    1016      7.00
     C    4830      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=7, symmetry=0
  Number of additional bonds: simple=7, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.66
  Conformation dependent library (CDL) restraints added in 324.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1436

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 0 sheets defined
      77.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 26
      removed outlier: 3.566A  pdb=" N   ILE A  24 " --> pdb=" O   HIS A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 38
    Processing helix  chain 'A' and resid 41 through 59
    Processing helix  chain 'A' and resid 64 through 88
    Processing helix  chain 'A' and resid 97 through 119
      removed outlier: 3.915A  pdb=" N   TRP A 101 " --> pdb=" O   HIS A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 134
    Processing helix  chain 'A' and resid 135 through 138
    Processing helix  chain 'A' and resid 160 through 165
      removed outlier: 3.618A  pdb=" N   HIS A 164 " --> pdb=" O   ARG A 160 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   PHE A 165 " --> pdb=" O   ILE A 161 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 160 through 165'
    Processing helix  chain 'A' and resid 166 through 184
    Processing helix  chain 'A' and resid 185 through 203
      removed outlier: 4.289A  pdb=" N   THR A 191 " --> pdb=" O   GLY A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 206
      No H-bonds generated for 'chain 'A' and resid 204 through 206'
    Processing helix  chain 'A' and resid 218 through 223
    Processing helix  chain 'A' and resid 224 through 243
    Processing helix  chain 'A' and resid 255 through 267
      removed outlier: 4.302A  pdb=" N   PHE A 267 " --> pdb=" O   ALA A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 312
    Processing helix  chain 'A' and resid 317 through 344
      removed outlier: 4.159A  pdb=" N   ARG A 323 " --> pdb=" O   LEU A 319 " (cutoff:3.500A)
      Proline residue:  A 333  - end of helix
    Processing helix  chain 'A' and resid 351 through 372
    Processing helix  chain 'A' and resid 381 through 408
      removed outlier: 4.173A  pdb=" N   LEU A 388 " --> pdb=" O   VAL A 384 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LEU A 399 " --> pdb=" O   THR A 395 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   TYR A 405 " --> pdb=" O   GLY A 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 26
      removed outlier: 3.632A  pdb=" N   ILE B  24 " --> pdb=" O   HIS B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 38
    Processing helix  chain 'B' and resid 43 through 59
      removed outlier: 3.501A  pdb=" N   THR B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 64 through 88
      removed outlier: 3.691A  pdb=" N   ILE B  69 " --> pdb=" O   PRO B  65 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE B  83 " --> pdb=" O   PHE B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 119
      removed outlier: 3.923A  pdb=" N   TRP B 101 " --> pdb=" O   HIS B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 134
    Processing helix  chain 'B' and resid 135 through 138
    Processing helix  chain 'B' and resid 160 through 165
      removed outlier: 3.603A  pdb=" N   HIS B 164 " --> pdb=" O   ARG B 160 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   PHE B 165 " --> pdb=" O   ILE B 161 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 160 through 165'
    Processing helix  chain 'B' and resid 166 through 184
      removed outlier: 3.651A  pdb=" N   LEU B 182 " --> pdb=" O   MET B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 203
      removed outlier: 4.329A  pdb=" N   THR B 191 " --> pdb=" O   GLY B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 206
      No H-bonds generated for 'chain 'B' and resid 204 through 206'
    Processing helix  chain 'B' and resid 213 through 217
    Processing helix  chain 'B' and resid 224 through 242
      removed outlier: 3.685A  pdb=" N   MET B 242 " --> pdb=" O   ARG B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 267
      removed outlier: 4.251A  pdb=" N   PHE B 267 " --> pdb=" O   ALA B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 311
      removed outlier: 3.560A  pdb=" N   LYS B 308 " --> pdb=" O   THR B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 344
      removed outlier: 4.246A  pdb=" N   ARG B 323 " --> pdb=" O   LEU B 319 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ALA B 332 " --> pdb=" O   GLY B 328 " (cutoff:3.500A)
      Proline residue:  B 333  - end of helix
      removed outlier: 3.650A  pdb=" N   ARG B 336 " --> pdb=" O   ALA B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 372
      removed outlier: 3.949A  pdb=" N   ALA B 365 " --> pdb=" O   GLY B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 408
      removed outlier: 4.230A  pdb=" N   LEU B 388 " --> pdb=" O   VAL B 384 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LEU B 399 " --> pdb=" O   THR B 395 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   TYR B 405 " --> pdb=" O   GLY B 401 " (cutoff:3.500A)

    414 hydrogen bonds defined for protein.
    1218 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: 0.96

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1028
        1.32 -     1.44: 2201
        1.44 -     1.57: 3953
        1.57 -     1.69: 32
        1.69 -     1.81: 62
  Bond restraints: 7276
  Sorted by residual:
  bond pdb=" CG1 ILE B 192 "
       pdb=" CD1 ILE B 192 "
    ideal  model  delta    sigma   weight residual
    1.513  1.467  0.046 3.90e-02 6.57e+02 1.37e+00
  bond pdb=" CA  ALA A 332 "
       pdb=" C   ALA A 332 "
    ideal  model  delta    sigma   weight residual
    1.521  1.533 -0.012 1.11e-02 8.12e+03 1.08e+00
  bond pdb=" CG1 ILE B 330 "
       pdb=" CD1 ILE B 330 "
    ideal  model  delta    sigma   weight residual
    1.513  1.472  0.041 3.90e-02 6.57e+02 1.08e+00
  bond pdb=" CG  LEU A  53 "
       pdb=" CD2 LEU A  53 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.06e+00
  bond pdb=" C   GLY A 328 "
       pdb=" O   GLY A 328 "
    ideal  model  delta    sigma   weight residual
    1.234  1.246 -0.012 1.19e-02 7.06e+03 9.48e-01
  ... (remaining 7271 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 9621
        1.98 -     3.97: 129
        3.97 -     5.95: 22
        5.95 -     7.93: 8
        7.93 -     9.92: 2
  Bond angle restraints: 9782
  Sorted by residual:
  angle pdb=" N   ILE A 381 "
        pdb=" CA  ILE A 381 "
        pdb=" C   ILE A 381 "
      ideal   model   delta    sigma   weight residual
     113.07  105.96    7.11 1.36e+00 5.41e-01 2.73e+01
  angle pdb=" C   LEU B 386 "
        pdb=" N   TRP B 387 "
        pdb=" CA  TRP B 387 "
      ideal   model   delta    sigma   weight residual
     121.58  111.66    9.92 1.95e+00 2.63e-01 2.59e+01
  angle pdb=" C   LEU A 386 "
        pdb=" N   TRP A 387 "
        pdb=" CA  TRP A 387 "
      ideal   model   delta    sigma   weight residual
     121.14  113.01    8.13 1.75e+00 3.27e-01 2.16e+01
  angle pdb=" N   ILE B 381 "
        pdb=" CA  ILE B 381 "
        pdb=" C   ILE B 381 "
      ideal   model   delta    sigma   weight residual
     112.98  107.20    5.78 1.25e+00 6.40e-01 2.14e+01
  angle pdb=" N   TRP B 387 "
        pdb=" CA  TRP B 387 "
        pdb=" CB  TRP B 387 "
      ideal   model   delta    sigma   weight residual
     110.41  117.34   -6.93 1.68e+00 3.54e-01 1.70e+01
  ... (remaining 9777 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.66: 3986
       35.66 -    71.33: 260
       71.33 -   106.99: 49
      106.99 -   142.66: 14
      142.66 -   178.32: 17
  Dihedral angle restraints: 4326
    sinusoidal: 2108
      harmonic: 2218
  Sorted by residual:
  dihedral pdb=" C7  T7X B 501 "
           pdb=" O13 T7X B 501 "
           pdb=" P1  T7X B 501 "
           pdb=" O11 T7X B 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -41.94  136.38 -178.32     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C7  T7X B 501 "
           pdb=" O13 T7X B 501 "
           pdb=" P1  T7X B 501 "
           pdb=" O12 T7X B 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      91.36  -92.00 -176.64     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" N1  LBN A 511 "
           pdb=" C6  LBN A 511 "
           pdb=" C9  LBN A 511 "
           pdb=" O2  LBN A 511 "
      ideal   model   delta sinusoidal    sigma   weight residual
      71.48 -104.18  175.66     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 4323 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 737
       0.045 -    0.090: 225
       0.090 -    0.135: 34
       0.135 -    0.181: 4
       0.181 -    0.226: 2
  Chirality restraints: 1002
  Sorted by residual:
  chirality pdb=" C1  T7X B 501 "
            pdb=" C2  T7X B 501 "
            pdb=" C6  T7X B 501 "
            pdb=" O1  T7X B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42   -2.19   -0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" C1  T7X A 510 "
            pdb=" C2  T7X A 510 "
            pdb=" C6  T7X A 510 "
            pdb=" O1  T7X A 510 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42   -2.23   -0.19 2.00e-01 2.50e+01 9.24e-01
  chirality pdb=" CA  ILE A 381 "
            pdb=" N   ILE A 381 "
            pdb=" C   ILE A 381 "
            pdb=" CB  ILE A 381 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.37e-01
  ... (remaining 999 not shown)

  Planarity restraints: 1126
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 387 "    0.023 2.00e-02 2.50e+03   2.82e-02 1.98e+01
        pdb=" CG  TRP B 387 "   -0.072 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 387 "    0.044 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 387 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 387 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 387 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 387 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 387 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 387 "    0.013 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 387 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 387 "   -0.024 2.00e-02 2.50e+03   2.76e-02 1.91e+01
        pdb=" CG  TRP A 387 "    0.072 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 387 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 387 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 387 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 387 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 387 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 387 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 387 "   -0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 387 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 184 "   -0.009 2.00e-02 2.50e+03   1.87e-02 3.51e+00
        pdb=" C   ARG B 184 "    0.032 2.00e-02 2.50e+03
        pdb=" O   ARG B 184 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER B 185 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1123 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 282
        2.72 -     3.27: 7096
        3.27 -     3.81: 11696
        3.81 -     4.36: 14283
        4.36 -     4.90: 24352
  Nonbonded interactions: 57709
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 265 "
            pdb=" OG1 THR B 268 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" OH  TYR A 291 "
            pdb=" O   LEU A 388 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OH  TYR B 291 "
            pdb=" O   LEU B 388 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OE1 GLU B 200 "
            pdb=" NE2 GLN B 217 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" O   TYR B  55 "
            pdb=" OG1 THR B  59 "
     model   vdw
     2.263 3.040
  ... (remaining 57704 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 14 through 408 or resid 502 or resid 504 or resid 508 thro \ 
ugh 509))
  selection = (chain 'B' and (resid 14 through 408 or resid 502 or (resid 504 and (name C1 or  \ 
name C12 or name C15 or name C18 or name C2 or name C25 or name C26 or name C27  \ 
or name C28 or name C29 or name C3 or name C30 or name C34 or name C35 or name C \ 
36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C6 or nam \ 
e C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name O5 or name O \ 
6 or name O7 or name O8 or name P1 )) or (resid 508 and (name C1 or name C10 or  \ 
name C12 or name C13 or name C15 or name C16 or name C18 or name C19 or name C2  \ 
or name C21 or name C25 or name C26 or name C27 or name C28 or name C29 or name  \ 
C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or na \ 
me C36 or name C37 or name C4 or name C6 or name C7 or name C9 or name N1 or nam \ 
e O1 or name O2 or name O3 or name O4 or name O5 or name O6 or name O7 or name O \ 
8 or name P1 )) or resid 509))
}

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:             1.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.670
  Find NCS groups from input model:        0.130
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
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      :  0.005   0.046   7283  Z= 0.200
  Angle     :  0.619   9.915   9782  Z= 0.323
  Chirality :  0.042   0.226   1002
  Planarity :  0.004   0.035   1126
  Dihedral  : 26.742 178.320   2890
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 22.27 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    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:  0.73 (0.31), residues: 746
  helix:  0.74 (0.22), residues: 530
  sheet:  None (None), residues: 0
  loop :  0.14 (0.45), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 276 
 TYR   0.020   0.001   TYR A 274 
 PHE   0.022   0.002   PHE A  79 
 TRP   0.072   0.003   TRP B 387 
 HIS   0.004   0.001   HIS A 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 7276)
  covalent geometry    : angle       0.61864 ( 9782)
  hydrogen bonds       : bond        0.20224 (  414)
  hydrogen bonds       : angle       7.28278 ( 1218)
  Misc. bond           : bond        0.00071 (    7)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 105
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 ASP cc_start: 0.8411 (t0) cc_final: 0.7857 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 106
  average time/residue: 0.0962
  time to fit residues: 13.6788
Evaluate side-chains
  102 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    0.1980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 298 GLN
A 309 HIS
** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.166672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.129381 restraints weight = 7698.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 1.89
r_work: 0.3107 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.1245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7283  Z= 0.128
  Angle     :  0.575   7.558   9782  Z= 0.281
  Chirality :  0.040   0.240   1002
  Planarity :  0.004   0.030   1126
  Dihedral  : 24.993 174.462   1483
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 20.06 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.31), residues: 746
  helix:  1.81 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop :  0.22 (0.45), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 276 
 TYR   0.008   0.001   TYR A 186 
 PHE   0.019   0.001   PHE A  79 
 TRP   0.056   0.002   TRP B 387 
 HIS   0.002   0.001   HIS B  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7276)
  covalent geometry    : angle       0.57495 ( 9782)
  hydrogen bonds       : bond        0.04371 (  414)
  hydrogen bonds       : angle       4.44776 ( 1218)
  Misc. bond           : bond        0.00036 (    7)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 ASP cc_start: 0.8606 (t0) cc_final: 0.8130 (t0)
REVERT: A  134 ASP cc_start: 0.8198 (t0) cc_final: 0.7906 (t0)
REVERT: A  184 ARG cc_start: 0.8709 (tpt170) cc_final: 0.8256 (tpp-160)
REVERT: A  276 ARG cc_start: 0.7893 (mmt180) cc_final: 0.7674 (mmt180)
REVERT: A  399 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.6883 (mp)
REVERT: B   31 ASP cc_start: 0.8764 (t0) cc_final: 0.8484 (t0)
REVERT: B  134 ASP cc_start: 0.8085 (t0) cc_final: 0.7748 (t0)
REVERT: B  184 ARG cc_start: 0.8793 (tpt-90) cc_final: 0.8215 (ttt90)
  outliers start: 25
  outliers final: 16
  residues processed: 124
  average time/residue: 0.0963
  time to fit residues: 15.8936
Evaluate side-chains
  116 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ILE
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  387 TRP
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain B residue   20 HIS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  298 GLN
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  387 TRP
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 13 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   chunk 5 optimal weight:    0.1980
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 309 HIS
** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 HIS
** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.164980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.127977 restraints weight = 7618.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 1.86
r_work: 0.3119 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7283  Z= 0.127
  Angle     :  0.533   6.838   9782  Z= 0.264
  Chirality :  0.039   0.227   1002
  Planarity :  0.003   0.026   1126
  Dihedral  : 23.356 172.440   1480
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 19.32 %
    Favored  : 76.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.45 (0.31), residues: 746
  helix:  2.18 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop :  0.21 (0.45), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 276 
 TYR   0.007   0.001   TYR A 186 
 PHE   0.016   0.001   PHE A  79 
 TRP   0.057   0.002   TRP B 387 
 HIS   0.002   0.000   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7276)
  covalent geometry    : angle       0.53260 ( 9782)
  hydrogen bonds       : bond        0.04081 (  414)
  hydrogen bonds       : angle       4.20616 ( 1218)
  Misc. bond           : bond        0.00030 (    7)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 ASP cc_start: 0.8502 (t0) cc_final: 0.7970 (t0)
REVERT: A  134 ASP cc_start: 0.8106 (t0) cc_final: 0.7760 (t0)
REVERT: A  184 ARG cc_start: 0.8695 (tpt170) cc_final: 0.8247 (tpp-160)
REVERT: A  242 MET cc_start: 0.8117 (mtt) cc_final: 0.7899 (mtp)
REVERT: A  276 ARG cc_start: 0.7799 (mmt180) cc_final: 0.7407 (mmt180)
REVERT: A  399 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.6885 (mp)
REVERT: B   31 ASP cc_start: 0.8675 (t0) cc_final: 0.8324 (t0)
REVERT: B  134 ASP cc_start: 0.8018 (t0) cc_final: 0.7624 (t0)
REVERT: B  184 ARG cc_start: 0.8769 (tpt-90) cc_final: 0.8266 (ttt90)
REVERT: B  278 PHE cc_start: 0.8608 (m-80) cc_final: 0.7959 (m-80)
  outliers start: 27
  outliers final: 19
  residues processed: 118
  average time/residue: 0.0951
  time to fit residues: 15.0286
Evaluate side-chains
  122 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   83 ILE
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  298 GLN
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  387 TRP
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain B residue   20 HIS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  298 GLN
Chi-restraints excluded: chain B residue  344 ASP
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 HIS
** B 353 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 = 0.3814 r_free = 0.3814 target = 0.163913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.126803 restraints weight = 7743.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 1.89
r_work: 0.3090 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7283  Z= 0.137
  Angle     :  0.557  13.974   9782  Z= 0.267
  Chirality :  0.040   0.200   1002
  Planarity :  0.003   0.025   1126
  Dihedral  : 22.702 170.743   1480
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 19.91 %
    Favored  : 75.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.52 (0.31), residues: 746
  helix:  2.26 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop :  0.14 (0.45), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 276 
 TYR   0.008   0.001   TYR A 245 
 PHE   0.017   0.001   PHE B 173 
 TRP   0.054   0.002   TRP A 387 
 HIS   0.004   0.001   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 7276)
  covalent geometry    : angle       0.55683 ( 9782)
  hydrogen bonds       : bond        0.04001 (  414)
  hydrogen bonds       : angle       4.10978 ( 1218)
  Misc. bond           : bond        0.00027 (    7)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 101
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.7246 (OUTLIER) cc_final: 0.4829 (m-10)
REVERT: A   31 ASP cc_start: 0.8522 (t0) cc_final: 0.7950 (t0)
REVERT: A  134 ASP cc_start: 0.8132 (t0) cc_final: 0.7776 (t0)
REVERT: A  184 ARG cc_start: 0.8690 (tpt170) cc_final: 0.8271 (tpp-160)
REVERT: A  242 MET cc_start: 0.8047 (mtt) cc_final: 0.7816 (mtp)
REVERT: A  276 ARG cc_start: 0.7801 (mmt180) cc_final: 0.7539 (mmt180)
REVERT: A  308 LYS cc_start: 0.7105 (tttp) cc_final: 0.6858 (ttpp)
REVERT: A  399 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.6943 (mp)
REVERT: B   17 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.5047 (m-10)
REVERT: B   31 ASP cc_start: 0.8645 (t0) cc_final: 0.8253 (t0)
REVERT: B  134 ASP cc_start: 0.8029 (t0) cc_final: 0.7621 (t0)
REVERT: B  266 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.6811 (tp40)
REVERT: B  278 PHE cc_start: 0.8577 (m-80) cc_final: 0.7947 (m-80)
  outliers start: 32
  outliers final: 26
  residues processed: 121
  average time/residue: 0.0942
  time to fit residues: 15.1020
Evaluate side-chains
  130 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 100
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   83 ILE
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  298 GLN
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  387 TRP
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   20 HIS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   83 ILE
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  298 GLN
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  344 ASP
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  387 TRP
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 64 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 309 HIS
** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 HIS
** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.159404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.121112 restraints weight = 7804.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 1.94
r_work: 0.3069 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.1646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7283  Z= 0.157
  Angle     :  0.570  12.871   9782  Z= 0.273
  Chirality :  0.040   0.202   1002
  Planarity :  0.003   0.025   1126
  Dihedral  : 22.270 167.520   1480
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 19.47 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.56 (0.31), residues: 746
  helix:  2.27 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop :  0.20 (0.45), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 276 
 TYR   0.010   0.001   TYR A 245 
 PHE   0.021   0.001   PHE A  79 
 TRP   0.054   0.002   TRP A 387 
 HIS   0.003   0.001   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 7276)
  covalent geometry    : angle       0.57027 ( 9782)
  hydrogen bonds       : bond        0.04152 (  414)
  hydrogen bonds       : angle       4.12386 ( 1218)
  Misc. bond           : bond        0.00029 (    7)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 99
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.4828 (m-10)
REVERT: A   31 ASP cc_start: 0.8560 (t0) cc_final: 0.7945 (t0)
REVERT: A  134 ASP cc_start: 0.8146 (t0) cc_final: 0.7748 (t0)
REVERT: A  184 ARG cc_start: 0.8717 (tpt170) cc_final: 0.8276 (tpp-160)
REVERT: A  242 MET cc_start: 0.8013 (mtt) cc_final: 0.7786 (mtp)
REVERT: A  266 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6567 (tt0)
REVERT: A  276 ARG cc_start: 0.7778 (mmt180) cc_final: 0.7397 (mpt180)
REVERT: A  399 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.6925 (mp)
REVERT: B   17 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.5127 (m-10)
REVERT: B   31 ASP cc_start: 0.8652 (t0) cc_final: 0.8201 (t0)
REVERT: B  134 ASP cc_start: 0.8069 (t0) cc_final: 0.7625 (t0)
REVERT: B  184 ARG cc_start: 0.8718 (tpt-90) cc_final: 0.8141 (ttt90)
REVERT: B  215 TRP cc_start: 0.6778 (p-90) cc_final: 0.6003 (p-90)
REVERT: B  266 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.6576 (tp40)
REVERT: B  399 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6850 (mp)
  outliers start: 38
  outliers final: 27
  residues processed: 123
  average time/residue: 0.0855
  time to fit residues: 14.0757
Evaluate side-chains
  131 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 98
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ASP
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   36 PHE
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   83 ILE
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  266 GLN
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  298 GLN
Chi-restraints excluded: chain A residue  309 HIS
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  387 TRP
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   20 HIS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   83 ILE
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  298 GLN
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  387 TRP
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  402 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 41 optimal weight:    0.2980
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   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 164 HIS
A 309 HIS
** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 HIS
** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.159224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.120593 restraints weight = 7820.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 1.97
r_work: 0.3092 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7283  Z= 0.122
  Angle     :  0.538  12.417   9782  Z= 0.260
  Chirality :  0.039   0.198   1002
  Planarity :  0.003   0.024   1126
  Dihedral  : 21.848 167.249   1480
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 20.06 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.66 (0.31), residues: 746
  helix:  2.35 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop :  0.23 (0.45), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 276 
 TYR   0.008   0.001   TYR A 245 
 PHE   0.019   0.001   PHE A  79 
 TRP   0.053   0.002   TRP A 387 
 HIS   0.004   0.001   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7276)
  covalent geometry    : angle       0.53788 ( 9782)
  hydrogen bonds       : bond        0.03880 (  414)
  hydrogen bonds       : angle       4.06388 ( 1218)
  Misc. bond           : bond        0.00032 (    7)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 103
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.4833 (m-10)
REVERT: A   31 ASP cc_start: 0.8539 (t0) cc_final: 0.7913 (t0)
REVERT: A  134 ASP cc_start: 0.8093 (t0) cc_final: 0.7706 (t0)
REVERT: A  182 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7749 (mm)
REVERT: A  184 ARG cc_start: 0.8687 (tpt170) cc_final: 0.8282 (tpp-160)
REVERT: A  242 MET cc_start: 0.8082 (mtt) cc_final: 0.7837 (mtp)
REVERT: A  276 ARG cc_start: 0.7754 (mmt180) cc_final: 0.7377 (mpt180)
REVERT: A  399 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6857 (mp)
REVERT: B   17 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.5090 (m-10)
REVERT: B   31 ASP cc_start: 0.8655 (t0) cc_final: 0.8170 (t0)
REVERT: B  134 ASP cc_start: 0.8042 (t0) cc_final: 0.7630 (t0)
REVERT: B  215 TRP cc_start: 0.6764 (p-90) cc_final: 0.5993 (p-90)
REVERT: B  266 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.6506 (tp40)
REVERT: B  399 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6841 (mp)
  outliers start: 37
  outliers final: 29
  residues processed: 126
  average time/residue: 0.0918
  time to fit residues: 15.4714
Evaluate side-chains
  136 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 101
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ASP
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   83 ILE
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  298 GLN
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  387 TRP
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   20 HIS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   83 ILE
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  298 GLN
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  344 ASP
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  387 TRP
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  402 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 58 optimal weight:    0.0670
   chunk 41 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   chunk 12 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 54 optimal weight:    0.3980
   chunk 66 optimal weight:    0.9980
   overall best weight:    0.8720

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

Flipped N/Q/H residues before XYZ refinement:
** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 HIS
** B 353 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 = 0.3793 r_free = 0.3793 target = 0.162061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.124202 restraints weight = 7675.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 1.93
r_work: 0.3082 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7283  Z= 0.135
  Angle     :  0.548  12.033   9782  Z= 0.263
  Chirality :  0.039   0.197   1002
  Planarity :  0.003   0.024   1126
  Dihedral  : 21.578 165.432   1480
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 19.03 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.67 (0.31), residues: 746
  helix:  2.35 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop :  0.26 (0.45), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 276 
 TYR   0.009   0.001   TYR A 245 
 PHE   0.018   0.001   PHE A  79 
 TRP   0.053   0.002   TRP A 387 
 HIS   0.003   0.000   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 7276)
  covalent geometry    : angle       0.54845 ( 9782)
  hydrogen bonds       : bond        0.03919 (  414)
  hydrogen bonds       : angle       4.04006 ( 1218)
  Misc. bond           : bond        0.00043 (    7)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 99
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.4837 (m-10)
REVERT: A   31 ASP cc_start: 0.8551 (t0) cc_final: 0.7913 (t0)
REVERT: A  134 ASP cc_start: 0.8143 (t0) cc_final: 0.7770 (t0)
REVERT: A  182 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7721 (mm)
REVERT: A  184 ARG cc_start: 0.8698 (tpt170) cc_final: 0.8347 (tpp-160)
REVERT: A  266 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6750 (tt0)
REVERT: A  276 ARG cc_start: 0.7774 (mmt180) cc_final: 0.7499 (mpt180)
REVERT: A  399 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.6912 (mp)
REVERT: B   17 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.5130 (m-10)
REVERT: B   31 ASP cc_start: 0.8675 (t0) cc_final: 0.8182 (t0)
REVERT: B  134 ASP cc_start: 0.8059 (t0) cc_final: 0.7685 (t0)
REVERT: B  184 ARG cc_start: 0.8681 (tpt-90) cc_final: 0.8050 (ttt90)
REVERT: B  215 TRP cc_start: 0.6759 (p-90) cc_final: 0.5970 (p-90)
REVERT: B  238 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6281 (tpp80)
REVERT: B  266 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.6633 (tp40)
REVERT: B  298 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7421 (mt0)
REVERT: B  399 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6883 (mp)
  outliers start: 41
  outliers final: 31
  residues processed: 126
  average time/residue: 0.0857
  time to fit residues: 14.4594
Evaluate side-chains
  138 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 98
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ASP
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   83 ILE
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  266 GLN
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  298 GLN
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  387 TRP
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   20 HIS
Chi-restraints excluded: chain B residue   83 ILE
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  238 ARG
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  298 GLN
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  344 ASP
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  387 TRP
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  402 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 71 optimal weight:    0.4980
   chunk 49 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 HIS
** B 353 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 = 0.3787 r_free = 0.3787 target = 0.161858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.123738 restraints weight = 7798.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.96
r_work: 0.3113 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7283  Z= 0.127
  Angle     :  0.536  11.855   9782  Z= 0.258
  Chirality :  0.039   0.199   1002
  Planarity :  0.003   0.031   1126
  Dihedral  : 20.999 164.130   1480
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 19.76 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.76 (0.31), residues: 746
  helix:  2.41 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop :  0.34 (0.46), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 276 
 TYR   0.007   0.001   TYR A 245 
 PHE   0.017   0.001   PHE A  79 
 TRP   0.052   0.002   TRP A 387 
 HIS   0.003   0.000   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7276)
  covalent geometry    : angle       0.53641 ( 9782)
  hydrogen bonds       : bond        0.03824 (  414)
  hydrogen bonds       : angle       4.00407 ( 1218)
  Misc. bond           : bond        0.00047 (    7)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 99
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.7266 (OUTLIER) cc_final: 0.4824 (m-10)
REVERT: A   31 ASP cc_start: 0.8557 (t0) cc_final: 0.7896 (t0)
REVERT: A  134 ASP cc_start: 0.8117 (t0) cc_final: 0.7746 (t0)
REVERT: A  182 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7739 (mm)
REVERT: A  184 ARG cc_start: 0.8704 (tpt170) cc_final: 0.8344 (tpp-160)
REVERT: A  266 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6847 (tt0)
REVERT: A  276 ARG cc_start: 0.7739 (mmt180) cc_final: 0.7488 (mpt180)
REVERT: A  399 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.6834 (mp)
REVERT: B   31 ASP cc_start: 0.8672 (t0) cc_final: 0.8163 (t0)
REVERT: B  134 ASP cc_start: 0.8048 (t0) cc_final: 0.7684 (t0)
REVERT: B  215 TRP cc_start: 0.6767 (p-90) cc_final: 0.5968 (p-90)
REVERT: B  238 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6063 (mpt180)
REVERT: B  266 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.6467 (tp40)
REVERT: B  298 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7521 (mt0)
REVERT: B  399 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6871 (mp)
  outliers start: 39
  outliers final: 28
  residues processed: 128
  average time/residue: 0.0918
  time to fit residues: 15.6237
Evaluate side-chains
  135 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 99
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ASP
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   83 ILE
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  266 GLN
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  298 GLN
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  387 TRP
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain B residue   14 ASP
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   20 HIS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   83 ILE
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  238 ARG
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  298 GLN
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  344 ASP
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  387 TRP
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 4 optimal weight:    0.0870
   chunk 11 optimal weight:    0.9980
   chunk 56 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0570
   overall best weight:    0.5476

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

Flipped N/Q/H residues before XYZ refinement:
** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 HIS
** B 353 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 = 0.3804 r_free = 0.3804 target = 0.162562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.124433 restraints weight = 7605.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 1.98
r_work: 0.3139 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7283  Z= 0.110
  Angle     :  0.533  14.065   9782  Z= 0.255
  Chirality :  0.039   0.191   1002
  Planarity :  0.003   0.025   1126
  Dihedral  : 20.649 162.345   1480
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 20.35 %
    Favored  : 74.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.89 (0.31), residues: 746
  helix:  2.50 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop :  0.39 (0.46), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 276 
 TYR   0.006   0.001   TYR A 186 
 PHE   0.016   0.001   PHE A  79 
 TRP   0.051   0.002   TRP A 387 
 HIS   0.002   0.000   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7276)
  covalent geometry    : angle       0.53297 ( 9782)
  hydrogen bonds       : bond        0.03660 (  414)
  hydrogen bonds       : angle       3.96483 ( 1218)
  Misc. bond           : bond        0.00036 (    7)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 105
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.4809 (m-10)
REVERT: A   31 ASP cc_start: 0.8577 (t0) cc_final: 0.7913 (t0)
REVERT: A  134 ASP cc_start: 0.8096 (t0) cc_final: 0.7701 (t0)
REVERT: A  184 ARG cc_start: 0.8593 (tpt170) cc_final: 0.8239 (tpp-160)
REVERT: A  276 ARG cc_start: 0.7752 (mmt180) cc_final: 0.7477 (mpt180)
REVERT: A  399 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.6830 (mp)
REVERT: B   31 ASP cc_start: 0.8655 (t0) cc_final: 0.8128 (t0)
REVERT: B  134 ASP cc_start: 0.8010 (t0) cc_final: 0.7719 (t0)
REVERT: B  184 ARG cc_start: 0.8763 (tpt-90) cc_final: 0.8065 (ttt90)
REVERT: B  217 GLN cc_start: 0.7300 (mm110) cc_final: 0.7093 (mm110)
REVERT: B  238 ARG cc_start: 0.6826 (OUTLIER) cc_final: 0.6349 (tpp80)
REVERT: B  266 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.6445 (tp40)
REVERT: B  278 PHE cc_start: 0.8433 (m-80) cc_final: 0.7906 (m-80)
REVERT: B  298 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7509 (mt0)
REVERT: B  399 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6790 (mp)
  outliers start: 34
  outliers final: 28
  residues processed: 128
  average time/residue: 0.0878
  time to fit residues: 15.0449
Evaluate side-chains
  132 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 98
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ASP
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   83 ILE
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  298 GLN
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  387 TRP
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   20 HIS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   83 ILE
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  238 ARG
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  298 GLN
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  344 ASP
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  387 TRP
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 25 optimal weight:    0.0040
   chunk 17 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.7192

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

Flipped N/Q/H residues before XYZ refinement:
** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 GLN
B 309 HIS
** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.160706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.122358 restraints weight = 7652.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 2.01
r_work: 0.3115 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7283  Z= 0.124
  Angle     :  0.543  13.944   9782  Z= 0.262
  Chirality :  0.039   0.198   1002
  Planarity :  0.003   0.026   1126
  Dihedral  : 20.483 160.778   1480
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 20.06 %
    Favored  : 74.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.90 (0.31), residues: 746
  helix:  2.50 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop :  0.42 (0.46), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 276 
 TYR   0.006   0.001   TYR A 245 
 PHE   0.017   0.001   PHE A  79 
 TRP   0.051   0.002   TRP A 387 
 HIS   0.003   0.000   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7276)
  covalent geometry    : angle       0.54333 ( 9782)
  hydrogen bonds       : bond        0.03764 (  414)
  hydrogen bonds       : angle       3.97582 ( 1218)
  Misc. bond           : bond        0.00033 (    7)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 100
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.4785 (m-10)
REVERT: A   31 ASP cc_start: 0.8590 (t0) cc_final: 0.7933 (t0)
REVERT: A  134 ASP cc_start: 0.8113 (t0) cc_final: 0.7724 (t0)
REVERT: A  184 ARG cc_start: 0.8625 (tpt170) cc_final: 0.8291 (tpp-160)
REVERT: A  266 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.6855 (tt0)
REVERT: A  276 ARG cc_start: 0.7747 (mmt180) cc_final: 0.7486 (mpt180)
REVERT: A  278 PHE cc_start: 0.8411 (m-80) cc_final: 0.7940 (m-80)
REVERT: A  399 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6716 (mp)
REVERT: B   31 ASP cc_start: 0.8667 (t0) cc_final: 0.8129 (t0)
REVERT: B  134 ASP cc_start: 0.7997 (t0) cc_final: 0.7656 (t0)
REVERT: B  184 ARG cc_start: 0.8739 (tpt-90) cc_final: 0.8046 (ttt90)
REVERT: B  217 GLN cc_start: 0.7246 (mm110) cc_final: 0.7041 (mm110)
REVERT: B  238 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.6339 (tpp80)
REVERT: B  266 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.6474 (tp40)
REVERT: B  278 PHE cc_start: 0.8431 (m-80) cc_final: 0.7896 (m-80)
REVERT: B  298 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7573 (mt0)
REVERT: B  399 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6809 (mp)
  outliers start: 36
  outliers final: 29
  residues processed: 124
  average time/residue: 0.0913
  time to fit residues: 15.1005
Evaluate side-chains
  136 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 100
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ASP
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   83 ILE
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  195 THR
Chi-restraints excluded: chain A residue  257 THR
Chi-restraints excluded: chain A residue  266 GLN
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  298 GLN
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  387 TRP
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  402 MET
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   20 HIS
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   83 ILE
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  235 VAL
Chi-restraints excluded: chain B residue  238 ARG
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  298 GLN
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  344 ASP
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  387 TRP
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  399 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0170
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 56 optimal weight:    6.9990
   chunk 42 optimal weight:    0.0370
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.5700

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

Flipped N/Q/H residues before XYZ refinement:
** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 309 HIS
** B 353 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 = 0.3868 r_free = 0.3868 target = 0.167778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.129780 restraints weight = 7485.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.00
r_work: 0.3167 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7283  Z= 0.110
  Angle     :  0.524  13.593   9782  Z= 0.253
  Chirality :  0.039   0.190   1002
  Planarity :  0.003   0.028   1126
  Dihedral  : 20.031 159.144   1480
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 20.06 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.98 (0.31), residues: 746
  helix:  2.58 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop :  0.40 (0.46), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 276 
 TYR   0.006   0.001   TYR B 186 
 PHE   0.015   0.001   PHE A  79 
 TRP   0.050   0.002   TRP A 387 
 HIS   0.002   0.000   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7276)
  covalent geometry    : angle       0.52357 ( 9782)
  hydrogen bonds       : bond        0.03573 (  414)
  hydrogen bonds       : angle       3.93052 ( 1218)
  Misc. bond           : bond        0.00036 (    7)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1814.20 seconds
wall clock time: 31 minutes 48.06 seconds (1908.06 seconds total)