Starting phenix.real_space_refine
on Sun Mar 10 19:27:31 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/03_2024/5ms1_3562.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/03_2024/5ms1_3562.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/03_2024/5ms1_3562.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/03_2024/5ms1_3562.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/03_2024/5ms1_3562.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ms1_3562/03_2024/5ms1_3562.pdb"
  }
  resolution = 4.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.028
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: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    2774      2.51       5
     N     732      2.21       5
     O     814      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR   52": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR   93": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  103": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  108": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  120": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  122": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE    6": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  100": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  127": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  248": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  264": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  268": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  277": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  278": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  281": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  288": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  299": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 4350
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1501
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1501
          Classifications: {'peptide': 189}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 170}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2849
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 2849
          Classifications: {'peptide': 367}
          Link IDs: {'PTRANS': 14, 'TRANS': 352}
  Time building chain proxies: 2.81, per 1000 atoms: 0.65
  Number of scatterers: 4350
  At special positions: 0
  Unit cell: (89.1, 85.8, 91.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O     814      8.00
     N     732      7.00
     C    2774      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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.68
  Conformation dependent library (CDL) restraints added in 769.0 milliseconds
  

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1034

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 9 sheets defined
      12.9% alpha, 46.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 54 through 61
    Processing helix  chain 'A' and resid 82 through 86
    Processing helix  chain 'A' and resid 137 through 141
    Processing helix  chain 'B' and resid 4 through 8
    Processing helix  chain 'B' and resid 48 through 52
    Processing helix  chain 'B' and resid 58 through 63
    Processing helix  chain 'B' and resid 103 through 108
    Processing helix  chain 'B' and resid 137 through 145
    Processing helix  chain 'B' and resid 230 through 237
    Processing helix  chain 'B' and resid 277 through 281
    Processing helix  chain 'B' and resid 300 through 304
    Processing helix  chain 'B' and resid 317 through 321
      removed outlier: 3.522A  pdb=" N   ASP B 321 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51
      removed outlier: 6.226A  pdb=" N   MET A 163 " --> pdb=" O   PRO A  13 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51
      removed outlier: 6.226A  pdb=" N   MET A 163 " --> pdb=" O   PRO A  13 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   ALA A  63 " --> pdb=" O   ASN A 174 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   ASN A 174 " --> pdb=" O   ALA A  63 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 41
      removed outlier: 3.734A  pdb=" N   ARG A 106 " --> pdb=" O   LEU A  94 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181
    Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 32
      removed outlier: 6.017A  pdb=" N   LYS B  24 " --> pdb=" O   ILE B 172 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   ILE B 172 " --> pdb=" O   LYS B  24 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 46
      removed outlier: 5.691A  pdb=" N   VAL B  41 " --> pdb=" O   CYS B 152 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   CYS B 152 " --> pdb=" O   VAL B  41 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   CYS B  87 " --> pdb=" O   VAL B 153 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ASP B 111 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 202
      removed outlier: 7.015A  pdb=" N   CYS B 187 " --> pdb=" O   CYS B 355 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   CYS B 355 " --> pdb=" O   CYS B 187 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ASN B 189 " --> pdb=" O   ASP B 353 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL B 349 " --> pdb=" O   LEU B 193 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   ARG B 195 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   LYS B 347 " --> pdb=" O   ARG B 195 " (cutoff:3.500A)
      removed outlier: 7.590A  pdb=" N   MET B 197 " --> pdb=" O   GLY B 345 " (cutoff:3.500A)
      removed outlier: 9.575A  pdb=" N   GLY B 345 " --> pdb=" O   MET B 197 " (cutoff:3.500A)
      removed outlier: 8.912A  pdb=" N   LYS B 199 " --> pdb=" O   ASN B 343 " (cutoff:3.500A)
      removed outlier: 8.191A  pdb=" N   ASN B 343 " --> pdb=" O   LYS B 199 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   VAL B 346 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   THR B 251 " --> pdb=" O   VAL B 346 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   LEU B 348 " --> pdb=" O   GLU B 249 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   GLU B 249 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   PHE B 354 " --> pdb=" O   ARG B 243 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ARG B 243 " --> pdb=" O   PHE B 354 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   GLY B 356 " --> pdb=" O   TYR B 241 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   TYR B 241 " --> pdb=" O   GLY B 356 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 202
      removed outlier: 7.015A  pdb=" N   CYS B 187 " --> pdb=" O   CYS B 355 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   CYS B 355 " --> pdb=" O   CYS B 187 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ASN B 189 " --> pdb=" O   ASP B 353 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL B 349 " --> pdb=" O   LEU B 193 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   ARG B 195 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   LYS B 347 " --> pdb=" O   ARG B 195 " (cutoff:3.500A)
      removed outlier: 7.590A  pdb=" N   MET B 197 " --> pdb=" O   GLY B 345 " (cutoff:3.500A)
      removed outlier: 9.575A  pdb=" N   GLY B 345 " --> pdb=" O   MET B 197 " (cutoff:3.500A)
      removed outlier: 8.912A  pdb=" N   LYS B 199 " --> pdb=" O   ASN B 343 " (cutoff:3.500A)
      removed outlier: 8.191A  pdb=" N   ASN B 343 " --> pdb=" O   LYS B 199 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   VAL B 346 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   THR B 251 " --> pdb=" O   VAL B 346 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   LEU B 348 " --> pdb=" O   GLU B 249 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   GLU B 249 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   PHE B 354 " --> pdb=" O   ARG B 243 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ARG B 243 " --> pdb=" O   PHE B 354 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   GLY B 356 " --> pdb=" O   TYR B 241 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   TYR B 241 " --> pdb=" O   GLY B 356 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 210 through 214

    179 hydrogen bonds defined for protein.
    447 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: 1.47

  Time building geometry restraints manager: 1.83 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: 1009
        1.32 -     1.45: 1181
        1.45 -     1.57: 2226
        1.57 -     1.69: 0
        1.69 -     1.82: 47
  Bond restraints: 4463
  Sorted by residual:
  bond pdb=" N   PRO B 282 "
       pdb=" CA  PRO B 282 "
    ideal  model  delta    sigma   weight residual
    1.467  1.415  0.052 1.21e-02 6.83e+03 1.83e+01
  bond pdb=" N   PRO A 181 "
       pdb=" CA  PRO A 181 "
    ideal  model  delta    sigma   weight residual
    1.466  1.418  0.048 1.19e-02 7.06e+03 1.59e+01
  bond pdb=" N   PRO A  41 "
       pdb=" CA  PRO A  41 "
    ideal  model  delta    sigma   weight residual
    1.466  1.420  0.045 1.19e-02 7.06e+03 1.44e+01
  bond pdb=" N   PRO A  13 "
       pdb=" CA  PRO A  13 "
    ideal  model  delta    sigma   weight residual
    1.467  1.421  0.046 1.21e-02 6.83e+03 1.44e+01
  bond pdb=" N   PRO B 214 "
       pdb=" CA  PRO B 214 "
    ideal  model  delta    sigma   weight residual
    1.467  1.423  0.044 1.21e-02 6.83e+03 1.34e+01
  ... (remaining 4458 not shown)

  Histogram of bond angle deviations from ideal:
       98.25 -   105.38: 119
      105.38 -   112.51: 2197
      112.51 -   119.64: 1503
      119.64 -   126.77: 2200
      126.77 -   133.90: 55
  Bond angle restraints: 6074
  Sorted by residual:
  angle pdb=" CA  ARG A  77 "
        pdb=" C   ARG A  77 "
        pdb=" O   ARG A  77 "
      ideal   model   delta    sigma   weight residual
     120.71  113.89    6.82 1.06e+00 8.90e-01 4.15e+01
  angle pdb=" C   PRO A  20 "
        pdb=" N   PRO A  21 "
        pdb=" CA  PRO A  21 "
      ideal   model   delta    sigma   weight residual
     120.03  126.37   -6.34 9.90e-01 1.02e+00 4.10e+01
  angle pdb=" C   GLY A 126 "
        pdb=" N   PRO A 127 "
        pdb=" CA  PRO A 127 "
      ideal   model   delta    sigma   weight residual
     119.64  125.65   -6.01 1.01e+00 9.80e-01 3.54e+01
  angle pdb=" C   PRO A  54 "
        pdb=" N   PRO A  55 "
        pdb=" CA  PRO A  55 "
      ideal   model   delta    sigma   weight residual
     119.32  125.73   -6.41 1.14e+00 7.69e-01 3.17e+01
  angle pdb=" C   THR A  19 "
        pdb=" N   PRO A  20 "
        pdb=" CA  PRO A  20 "
      ideal   model   delta    sigma   weight residual
     119.66  123.52   -3.86 7.30e-01 1.88e+00 2.79e+01
  ... (remaining 6069 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.74: 2555
       16.74 -    33.48: 41
       33.48 -    50.22: 15
       50.22 -    66.96: 9
       66.96 -    83.70: 4
  Dihedral angle restraints: 2624
    sinusoidal: 1022
      harmonic: 1602
  Sorted by residual:
  dihedral pdb=" CA  ARG A  77 "
           pdb=" C   ARG A  77 "
           pdb=" N   GLY A  78 "
           pdb=" CA  GLY A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   37.92  -37.92     0      5.00e+00 4.00e-02 5.75e+01
  dihedral pdb=" CG  ARG A 154 "
           pdb=" CD  ARG A 154 "
           pdb=" NE  ARG A 154 "
           pdb=" CZ  ARG A 154 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -130.34   40.34     2      1.50e+01 4.44e-03 8.94e+00
  dihedral pdb=" CA  ASP A 166 "
           pdb=" CB  ASP A 166 "
           pdb=" CG  ASP A 166 "
           pdb=" OD1 ASP A 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -80.90   50.90     1      2.00e+01 2.50e-03 8.86e+00
  ... (remaining 2621 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 410
       0.058 -    0.117: 199
       0.117 -    0.175: 51
       0.175 -    0.234: 12
       0.234 -    0.292: 1
  Chirality restraints: 673
  Sorted by residual:
  chirality pdb=" CA  MET B 231 "
            pdb=" N   MET B 231 "
            pdb=" C   MET B 231 "
            pdb=" CB  MET B 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.13e+00
  chirality pdb=" CA  SER B 309 "
            pdb=" N   SER B 309 "
            pdb=" C   SER B 309 "
            pdb=" CB  SER B 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  LEU B 184 "
            pdb=" N   LEU B 184 "
            pdb=" C   LEU B 184 "
            pdb=" CB  LEU B 184 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.74e-01
  ... (remaining 670 not shown)

  Planarity restraints: 782
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A  77 "    0.059 2.00e-02 2.50e+03   1.20e-01 1.43e+02
        pdb=" C   ARG A  77 "   -0.207 2.00e-02 2.50e+03
        pdb=" O   ARG A  77 "    0.077 2.00e-02 2.50e+03
        pdb=" N   GLY A  78 "    0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  47 "   -0.036 2.00e-02 2.50e+03   1.74e-02 7.60e+00
        pdb=" CG  TRP A  47 "    0.019 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  47 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  47 "    0.018 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  47 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  47 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  47 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  47 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  47 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  47 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 130 "    0.036 5.00e-02 4.00e+02   5.84e-02 5.46e+00
        pdb=" N   PRO B 131 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO B 131 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 131 "    0.031 5.00e-02 4.00e+02
  ... (remaining 779 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 1966
        2.91 -     3.41: 3911
        3.41 -     3.91: 7317
        3.91 -     4.40: 8459
        4.40 -     4.90: 13903
  Nonbonded interactions: 35556
  Sorted by model distance:
  nonbonded pdb=" N   GLU B 279 "
            pdb=" OE1 GLU B 279 "
     model   vdw
     2.413 2.520
  nonbonded pdb=" OG  SER B 366 "
            pdb=" N   ARG B 367 "
     model   vdw
     2.438 2.520
  nonbonded pdb=" O   SER A 183 "
            pdb=" OG1 THR A 184 "
     model   vdw
     2.439 2.440
  nonbonded pdb=" N   GLU A 101 "
            pdb=" OE1 GLU A 101 "
     model   vdw
     2.442 2.520
  nonbonded pdb=" OG1 THR B 224 "
            pdb=" N   GLN B 225 "
     model   vdw
     2.474 2.520
  ... (remaining 35551 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          19.920
  Check model and map are aligned:         0.070
  Set scattering table:                    0.040
  Process input model:                     16.630
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
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      :  0.014   0.058   4463  Z= 0.906
  Angle     :  1.510   8.431   6074  Z= 1.007
  Chirality :  0.071   0.292    673
  Planarity :  0.008   0.120    782
  Dihedral  :  9.301  83.699   1590
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 2.10
  Ramachandran Plot:
    Outliers :  1.09 %
    Allowed  :  5.45 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.34), residues: 550
  helix: -3.05 (0.45), residues: 53
  sheet:  1.15 (0.36), residues: 192
  loop : -1.24 (0.33), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.006   TRP A  47 
 HIS   0.004   0.001   HIS A  50 
 PHE   0.026   0.004   PHE B 125 
 TYR   0.021   0.005   TYR B 278 
 ARG   0.004   0.001   ARG B 367 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.490 
Fit side-chains
REVERT: A   20 PRO cc_start: 0.9118 (Cg_exo) cc_final: 0.8803 (Cg_endo)
REVERT: A   39 ILE cc_start: 0.8932 (mt) cc_final: 0.8720 (mt)
REVERT: A   49 THR cc_start: 0.9359 (p) cc_final: 0.9002 (t)
REVERT: A   75 ASN cc_start: 0.7730 (m-40) cc_final: 0.7429 (m-40)
REVERT: A   82 LYS cc_start: 0.8103 (mttt) cc_final: 0.7096 (mmmt)
REVERT: A  113 PRO cc_start: 0.8812 (Cg_exo) cc_final: 0.8540 (Cg_endo)
REVERT: A  195 ARG cc_start: 0.5271 (mtm-85) cc_final: 0.5049 (mtt180)
REVERT: B   31 LEU cc_start: 0.8037 (tp) cc_final: 0.7695 (tt)
REVERT: B   87 CYS cc_start: 0.8880 (t) cc_final: 0.8182 (t)
REVERT: B  111 ASP cc_start: 0.8767 (m-30) cc_final: 0.8260 (m-30)
REVERT: B  116 ASN cc_start: 0.8548 (t0) cc_final: 0.8107 (t0)
REVERT: B  134 ASP cc_start: 0.7940 (p0) cc_final: 0.7696 (p0)
REVERT: B  152 CYS cc_start: 0.7941 (t) cc_final: 0.7079 (t)
REVERT: B  153 VAL cc_start: 0.8200 (t) cc_final: 0.7910 (t)
REVERT: B  259 LYS cc_start: 0.8547 (mttt) cc_final: 0.6947 (pttp)
REVERT: B  261 THR cc_start: 0.8227 (m) cc_final: 0.7930 (p)
REVERT: B  351 ILE cc_start: 0.7416 (mt) cc_final: 0.7107 (mt)
REVERT: B  353 ASP cc_start: 0.8361 (t0) cc_final: 0.8037 (t0)
REVERT: B  360 ASN cc_start: 0.9000 (t0) cc_final: 0.8683 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.1814
  time to fit residues: 38.1258
Evaluate side-chains
  100 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 31 optimal weight:    0.2980
   chunk 49 optimal weight:    3.9990
   overall best weight:    1.8588

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

Flipped N/Q/H residues before XYZ refinement:
A  89 GLN
A 119 ASN
A 157 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4463  Z= 0.258
  Angle     :  0.625   7.244   6074  Z= 0.341
  Chirality :  0.046   0.172    673
  Planarity :  0.005   0.047    782
  Dihedral  :  4.646  19.509    594
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.36 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.34), residues: 550
  helix: -1.62 (0.67), residues: 48
  sheet:  1.05 (0.37), residues: 195
  loop : -0.75 (0.32), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A  47 
 HIS   0.001   0.000   HIS B 283 
 PHE   0.017   0.002   PHE B 275 
 TYR   0.011   0.001   TYR B 241 
 ARG   0.004   0.001   ARG A  61 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 LYS cc_start: 0.8360 (mttt) cc_final: 0.7420 (mmmt)
REVERT: A  112 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8703 (tt0)
REVERT: A  113 PRO cc_start: 0.9090 (Cg_exo) cc_final: 0.8769 (Cg_endo)
REVERT: B   50 VAL cc_start: 0.8214 (t) cc_final: 0.7895 (p)
REVERT: B   87 CYS cc_start: 0.8966 (t) cc_final: 0.8556 (t)
REVERT: B   92 ILE cc_start: 0.9164 (mm) cc_final: 0.8912 (mm)
REVERT: B   99 LYS cc_start: 0.8528 (mmmt) cc_final: 0.8104 (mtmm)
REVERT: B  111 ASP cc_start: 0.8873 (m-30) cc_final: 0.8355 (m-30)
REVERT: B  116 ASN cc_start: 0.9120 (t0) cc_final: 0.8629 (t0)
REVERT: B  132 CYS cc_start: 0.8938 (p) cc_final: 0.8435 (p)
REVERT: B  153 VAL cc_start: 0.8289 (t) cc_final: 0.8058 (t)
REVERT: B  239 TRP cc_start: 0.8838 (m-90) cc_final: 0.8385 (m100)
REVERT: B  253 MET cc_start: 0.8904 (mtm) cc_final: 0.8679 (mtm)
REVERT: B  259 LYS cc_start: 0.8560 (mttt) cc_final: 0.7044 (pttp)
REVERT: B  351 ILE cc_start: 0.7431 (mt) cc_final: 0.7062 (mt)
REVERT: B  353 ASP cc_start: 0.8574 (t0) cc_final: 0.8242 (t0)
REVERT: B  360 ASN cc_start: 0.9098 (t0) cc_final: 0.8732 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1250
  time to fit residues: 22.5890
Evaluate side-chains
  107 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 15 optimal weight:    8.9990
   chunk 40 optimal weight:    9.9990
   chunk 33 optimal weight:    0.2980
   chunk 13 optimal weight:    0.9980
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 43 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
B 225 GLN
B 287 GLN
B 302 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.3850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4463  Z= 0.234
  Angle     :  0.574   6.914   6074  Z= 0.309
  Chirality :  0.045   0.159    673
  Planarity :  0.005   0.040    782
  Dihedral  :  4.422  15.821    594
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.09 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.35), residues: 550
  helix: -1.05 (0.71), residues: 47
  sheet:  0.92 (0.39), residues: 190
  loop : -0.63 (0.33), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 156 
 HIS   0.004   0.001   HIS B 331 
 PHE   0.025   0.002   PHE B 275 
 TYR   0.015   0.001   TYR B 241 
 ARG   0.005   0.001   ARG A 106 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.429 
Fit side-chains
REVERT: A   52 TYR cc_start: 0.8379 (m-80) cc_final: 0.8060 (m-10)
REVERT: A   75 ASN cc_start: 0.8279 (m-40) cc_final: 0.7941 (m-40)
REVERT: A   82 LYS cc_start: 0.8506 (mttt) cc_final: 0.7694 (mmmt)
REVERT: A  112 GLN cc_start: 0.9145 (mm-40) cc_final: 0.8704 (tt0)
REVERT: A  113 PRO cc_start: 0.9116 (Cg_exo) cc_final: 0.8808 (Cg_endo)
REVERT: A  118 LEU cc_start: 0.8297 (tt) cc_final: 0.8061 (tt)
REVERT: A  165 PHE cc_start: 0.9313 (m-10) cc_final: 0.8896 (m-80)
REVERT: B   99 LYS cc_start: 0.8652 (mmmt) cc_final: 0.8216 (mtmm)
REVERT: B  102 THR cc_start: 0.8870 (p) cc_final: 0.8663 (t)
REVERT: B  110 GLN cc_start: 0.8404 (tt0) cc_final: 0.7937 (tt0)
REVERT: B  111 ASP cc_start: 0.8965 (m-30) cc_final: 0.8358 (m-30)
REVERT: B  115 TRP cc_start: 0.8115 (p90) cc_final: 0.7508 (p-90)
REVERT: B  116 ASN cc_start: 0.9277 (t0) cc_final: 0.8978 (t0)
REVERT: B  134 ASP cc_start: 0.8326 (p0) cc_final: 0.7942 (p0)
REVERT: B  152 CYS cc_start: 0.7926 (t) cc_final: 0.6802 (t)
REVERT: B  178 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8548 (mt-10)
REVERT: B  236 ILE cc_start: 0.9007 (tt) cc_final: 0.8727 (tt)
REVERT: B  239 TRP cc_start: 0.9014 (m-90) cc_final: 0.8337 (m100)
REVERT: B  259 LYS cc_start: 0.8699 (mttt) cc_final: 0.7165 (pttm)
REVERT: B  271 LEU cc_start: 0.8757 (tp) cc_final: 0.8384 (tt)
REVERT: B  353 ASP cc_start: 0.8601 (t0) cc_final: 0.8191 (t0)
REVERT: B  360 ASN cc_start: 0.9310 (t0) cc_final: 0.8990 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1315
  time to fit residues: 22.3146
Evaluate side-chains
  105 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 36 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 32 optimal weight:    9.9990
   chunk 49 optimal weight:    7.9990
   chunk 52 optimal weight:    9.9990
   chunk 46 optimal weight:    3.9990
   chunk 14 optimal weight:    7.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.4348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4463  Z= 0.217
  Angle     :  0.568   6.474   6074  Z= 0.299
  Chirality :  0.045   0.157    673
  Planarity :  0.004   0.039    782
  Dihedral  :  4.212  17.248    594
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.73 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.35), residues: 550
  helix: -1.03 (0.70), residues: 48
  sheet:  0.97 (0.39), residues: 187
  loop : -0.62 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 170 
 HIS   0.003   0.001   HIS B 283 
 PHE   0.019   0.002   PHE B 275 
 TYR   0.021   0.002   TYR B 278 
 ARG   0.003   0.000   ARG B 367 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.552 
Fit side-chains
REVERT: A   75 ASN cc_start: 0.8431 (m-40) cc_final: 0.8163 (m-40)
REVERT: A   82 LYS cc_start: 0.8653 (mttt) cc_final: 0.8014 (mmmt)
REVERT: A  112 GLN cc_start: 0.9151 (mm-40) cc_final: 0.8714 (tt0)
REVERT: A  113 PRO cc_start: 0.8924 (Cg_exo) cc_final: 0.8602 (Cg_endo)
REVERT: A  118 LEU cc_start: 0.8154 (tt) cc_final: 0.7779 (tt)
REVERT: A  165 PHE cc_start: 0.9282 (m-10) cc_final: 0.8926 (m-10)
REVERT: B   43 LEU cc_start: 0.8685 (tp) cc_final: 0.8457 (tp)
REVERT: B   47 LEU cc_start: 0.8990 (tt) cc_final: 0.8750 (tt)
REVERT: B   99 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8361 (mtmm)
REVERT: B  115 TRP cc_start: 0.8240 (p90) cc_final: 0.7579 (p-90)
REVERT: B  116 ASN cc_start: 0.9362 (t0) cc_final: 0.8998 (t0)
REVERT: B  134 ASP cc_start: 0.8411 (p0) cc_final: 0.8050 (p0)
REVERT: B  152 CYS cc_start: 0.8147 (t) cc_final: 0.6890 (t)
REVERT: B  178 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8624 (mt-10)
REVERT: B  236 ILE cc_start: 0.9058 (tt) cc_final: 0.8828 (tt)
REVERT: B  239 TRP cc_start: 0.8966 (m-90) cc_final: 0.8430 (m100)
REVERT: B  259 LYS cc_start: 0.8782 (mttt) cc_final: 0.7223 (pttm)
REVERT: B  271 LEU cc_start: 0.8784 (tp) cc_final: 0.8318 (tt)
REVERT: B  279 GLU cc_start: 0.9301 (mm-30) cc_final: 0.8596 (mm-30)
REVERT: B  353 ASP cc_start: 0.8574 (t0) cc_final: 0.8166 (t0)
REVERT: B  360 ASN cc_start: 0.9384 (t0) cc_final: 0.9096 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1162
  time to fit residues: 19.4448
Evaluate side-chains
  98 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 36 optimal weight:   10.0000
   chunk 26 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 17 optimal weight:   10.0000
   chunk 47 optimal weight:    5.9990
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 GLN
** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 343 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.4944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   4463  Z= 0.265
  Angle     :  0.587   6.528   6074  Z= 0.309
  Chirality :  0.045   0.147    673
  Planarity :  0.004   0.037    782
  Dihedral  :  4.245  16.320    594
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.27 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.35), residues: 550
  helix: -1.09 (0.67), residues: 54
  sheet:  1.00 (0.38), residues: 192
  loop : -0.64 (0.33), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 115 
 HIS   0.003   0.001   HIS B 283 
 PHE   0.018   0.002   PHE B 275 
 TYR   0.028   0.002   TYR B 278 
 ARG   0.004   0.000   ARG A 106 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 LYS cc_start: 0.8660 (mttt) cc_final: 0.8034 (mmmt)
REVERT: A  112 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8718 (tt0)
REVERT: A  113 PRO cc_start: 0.8688 (Cg_exo) cc_final: 0.8335 (Cg_endo)
REVERT: A  118 LEU cc_start: 0.8245 (tt) cc_final: 0.7833 (tt)
REVERT: A  165 PHE cc_start: 0.9263 (m-10) cc_final: 0.8997 (m-10)
REVERT: B   99 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8310 (mtmm)
REVERT: B  113 MET cc_start: 0.7287 (ttp) cc_final: 0.6953 (tpp)
REVERT: B  116 ASN cc_start: 0.9412 (t0) cc_final: 0.8735 (t0)
REVERT: B  123 PHE cc_start: 0.7674 (t80) cc_final: 0.7411 (t80)
REVERT: B  152 CYS cc_start: 0.8189 (t) cc_final: 0.7214 (t)
REVERT: B  178 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8678 (mt-10)
REVERT: B  206 VAL cc_start: 0.8551 (m) cc_final: 0.8213 (p)
REVERT: B  259 LYS cc_start: 0.8883 (mttt) cc_final: 0.7275 (pttm)
REVERT: B  271 LEU cc_start: 0.8791 (tp) cc_final: 0.8129 (tt)
REVERT: B  279 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8592 (mm-30)
REVERT: B  321 ASP cc_start: 0.9146 (t0) cc_final: 0.8740 (t0)
REVERT: B  353 ASP cc_start: 0.8663 (t0) cc_final: 0.8235 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1397
  time to fit residues: 22.4208
Evaluate side-chains
  96 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 52 optimal weight:   10.0000
   chunk 43 optimal weight:    7.9990
   chunk 24 optimal weight:    0.5980
   chunk 4 optimal weight:    9.9990
   chunk 17 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN
** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 233 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.5273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4463  Z= 0.194
  Angle     :  0.552   6.478   6074  Z= 0.288
  Chirality :  0.045   0.145    673
  Planarity :  0.004   0.038    782
  Dihedral  :  4.115  15.919    594
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.27 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.08 %
    Favored  : 97.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.35), residues: 550
  helix: -1.01 (0.70), residues: 48
  sheet:  1.11 (0.38), residues: 192
  loop : -0.63 (0.33), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  47 
 HIS   0.003   0.001   HIS B 283 
 PHE   0.017   0.002   PHE B 275 
 TYR   0.009   0.001   TYR A  52 
 ARG   0.005   0.000   ARG A  61 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 LYS cc_start: 0.8730 (mttt) cc_final: 0.8135 (mmmt)
REVERT: A  112 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8797 (tt0)
REVERT: A  113 PRO cc_start: 0.8697 (Cg_exo) cc_final: 0.8355 (Cg_endo)
REVERT: B   99 LYS cc_start: 0.8686 (mmmt) cc_final: 0.8272 (mtmm)
REVERT: B  116 ASN cc_start: 0.9467 (t0) cc_final: 0.8979 (t0)
REVERT: B  152 CYS cc_start: 0.8264 (t) cc_final: 0.7315 (t)
REVERT: B  178 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8694 (mt-10)
REVERT: B  189 ASN cc_start: 0.8854 (m-40) cc_final: 0.8182 (t0)
REVERT: B  206 VAL cc_start: 0.8651 (m) cc_final: 0.8311 (p)
REVERT: B  213 MET cc_start: 0.8650 (mmm) cc_final: 0.8399 (mmm)
REVERT: B  259 LYS cc_start: 0.8967 (mttt) cc_final: 0.7374 (pttp)
REVERT: B  271 LEU cc_start: 0.8769 (tp) cc_final: 0.8260 (tt)
REVERT: B  321 ASP cc_start: 0.9081 (t0) cc_final: 0.8736 (t0)
REVERT: B  353 ASP cc_start: 0.8660 (t0) cc_final: 0.8243 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1344
  time to fit residues: 20.9078
Evaluate side-chains
  94 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   chunk 43 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:    0.4980
   chunk 24 optimal weight:    0.7980
   chunk 20 optimal weight:    9.9990
   chunk 15 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    2.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 GLN
** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.5753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4463  Z= 0.267
  Angle     :  0.594   7.638   6074  Z= 0.311
  Chirality :  0.045   0.142    673
  Planarity :  0.004   0.038    782
  Dihedral  :  4.310  14.214    594
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.35), residues: 550
  helix: -0.95 (0.73), residues: 47
  sheet:  0.99 (0.39), residues: 188
  loop : -0.66 (0.33), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 196 
 HIS   0.003   0.001   HIS B 283 
 PHE   0.018   0.002   PHE B  62 
 TYR   0.025   0.002   TYR B 278 
 ARG   0.004   0.001   ARG A  61 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A   82 LYS cc_start: 0.8778 (mttt) cc_final: 0.8148 (mmmt)
REVERT: A  112 GLN cc_start: 0.9163 (mm-40) cc_final: 0.8773 (tt0)
REVERT: A  113 PRO cc_start: 0.8640 (Cg_exo) cc_final: 0.8294 (Cg_endo)
REVERT: B   99 LYS cc_start: 0.8745 (mmmt) cc_final: 0.8274 (mtmm)
REVERT: B  116 ASN cc_start: 0.9555 (t0) cc_final: 0.8956 (t0)
REVERT: B  152 CYS cc_start: 0.8628 (t) cc_final: 0.7967 (t)
REVERT: B  178 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8766 (mt-10)
REVERT: B  189 ASN cc_start: 0.8921 (m-40) cc_final: 0.8338 (t0)
REVERT: B  206 VAL cc_start: 0.8758 (m) cc_final: 0.8417 (p)
REVERT: B  213 MET cc_start: 0.8694 (mmm) cc_final: 0.8409 (mmm)
REVERT: B  259 LYS cc_start: 0.9017 (mttt) cc_final: 0.7374 (pttm)
REVERT: B  271 LEU cc_start: 0.8740 (tp) cc_final: 0.8020 (tt)
REVERT: B  321 ASP cc_start: 0.9074 (t0) cc_final: 0.8834 (t0)
REVERT: B  353 ASP cc_start: 0.8755 (t0) cc_final: 0.8330 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1234
  time to fit residues: 19.2331
Evaluate side-chains
  89 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 45 optimal weight:    1.9990
   chunk 48 optimal weight:    0.3980
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   overall best weight:    1.6788

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

Flipped N/Q/H residues before XYZ refinement:
** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 GLN
** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 233 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.6040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4463  Z= 0.211
  Angle     :  0.572   8.067   6074  Z= 0.297
  Chirality :  0.045   0.143    673
  Planarity :  0.004   0.037    782
  Dihedral  :  4.201  13.782    594
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.83 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.36), residues: 550
  helix: -1.38 (0.67), residues: 53
  sheet:  0.96 (0.39), residues: 192
  loop : -0.79 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 115 
 HIS   0.002   0.001   HIS B 283 
 PHE   0.016   0.002   PHE B  62 
 TYR   0.006   0.001   TYR B 327 
 ARG   0.004   0.000   ARG A  61 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 LYS cc_start: 0.8791 (mttt) cc_final: 0.8122 (mmmt)
REVERT: A  112 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8770 (tt0)
REVERT: A  113 PRO cc_start: 0.8710 (Cg_exo) cc_final: 0.8381 (Cg_endo)
REVERT: B   46 TYR cc_start: 0.8785 (m-80) cc_final: 0.8437 (m-80)
REVERT: B   93 ASN cc_start: 0.9527 (m110) cc_final: 0.9258 (m110)
REVERT: B  116 ASN cc_start: 0.9573 (t0) cc_final: 0.9012 (t0)
REVERT: B  178 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8768 (mt-10)
REVERT: B  189 ASN cc_start: 0.8905 (m-40) cc_final: 0.8320 (t0)
REVERT: B  206 VAL cc_start: 0.8802 (m) cc_final: 0.8475 (p)
REVERT: B  213 MET cc_start: 0.8677 (mmm) cc_final: 0.8374 (mmm)
REVERT: B  259 LYS cc_start: 0.9048 (mttt) cc_final: 0.7404 (pttm)
REVERT: B  271 LEU cc_start: 0.8712 (tp) cc_final: 0.8173 (tt)
REVERT: B  321 ASP cc_start: 0.9101 (t0) cc_final: 0.8828 (t0)
REVERT: B  353 ASP cc_start: 0.8789 (t0) cc_final: 0.8391 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 108
  average time/residue: 0.1375
  time to fit residues: 19.7912
Evaluate side-chains
  90 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 43 optimal weight:    0.0270
   chunk 45 optimal weight:    0.0970
   chunk 48 optimal weight:    0.7980
   chunk 31 optimal weight:    8.9990
   chunk 51 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.3840

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

Flipped N/Q/H residues before XYZ refinement:
** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 GLN
** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 313 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.6215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   4463  Z= 0.201
  Angle     :  0.578   9.016   6074  Z= 0.297
  Chirality :  0.045   0.148    673
  Planarity :  0.004   0.045    782
  Dihedral  :  4.180  15.955    594
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.36), residues: 550
  helix: -1.34 (0.72), residues: 47
  sheet:  0.98 (0.39), residues: 192
  loop : -0.93 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 115 
 HIS   0.002   0.001   HIS B 331 
 PHE   0.016   0.002   PHE B 275 
 TYR   0.025   0.001   TYR B 278 
 ARG   0.004   0.000   ARG A  61 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.452 
Fit side-chains
REVERT: A   48 ASN cc_start: 0.8258 (t0) cc_final: 0.7546 (t0)
REVERT: A   82 LYS cc_start: 0.8815 (mttt) cc_final: 0.8173 (mmmt)
REVERT: A  112 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8773 (tt0)
REVERT: A  113 PRO cc_start: 0.8695 (Cg_exo) cc_final: 0.8365 (Cg_endo)
REVERT: B   46 TYR cc_start: 0.8865 (m-80) cc_final: 0.8540 (m-80)
REVERT: B   93 ASN cc_start: 0.9540 (m110) cc_final: 0.9266 (m110)
REVERT: B  116 ASN cc_start: 0.9572 (t0) cc_final: 0.9070 (t0)
REVERT: B  152 CYS cc_start: 0.8554 (t) cc_final: 0.8043 (t)
REVERT: B  165 ILE cc_start: 0.9153 (mt) cc_final: 0.8821 (mm)
REVERT: B  178 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8767 (mt-10)
REVERT: B  189 ASN cc_start: 0.8869 (m-40) cc_final: 0.8251 (t0)
REVERT: B  206 VAL cc_start: 0.8818 (m) cc_final: 0.8473 (p)
REVERT: B  213 MET cc_start: 0.8749 (mmm) cc_final: 0.8451 (mmm)
REVERT: B  259 LYS cc_start: 0.9032 (mttt) cc_final: 0.7387 (pttm)
REVERT: B  271 LEU cc_start: 0.8748 (tp) cc_final: 0.8069 (tt)
REVERT: B  321 ASP cc_start: 0.9068 (t0) cc_final: 0.8796 (t0)
REVERT: B  353 ASP cc_start: 0.8800 (t0) cc_final: 0.8390 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1138
  time to fit residues: 16.3586
Evaluate side-chains
  84 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 33 optimal weight:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 45 optimal weight:    1.9990
   chunk 13 optimal weight:    8.9990
   chunk 39 optimal weight:    0.7980
   chunk 6 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 GLN
B 128 ASN
** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.6461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4463  Z= 0.242
  Angle     :  0.585  10.615   6074  Z= 0.301
  Chirality :  0.045   0.150    673
  Planarity :  0.004   0.046    782
  Dihedral  :  4.181  14.167    594
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  0.83 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.36), residues: 550
  helix: -1.54 (0.67), residues: 51
  sheet:  1.06 (0.39), residues: 193
  loop : -0.97 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 115 
 HIS   0.002   0.001   HIS A  71 
 PHE   0.019   0.002   PHE B  62 
 TYR   0.006   0.001   TYR B 327 
 ARG   0.005   0.000   ARG A  61 

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

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

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1100 Ramachandran restraints generated.
    550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.442 
Fit side-chains
REVERT: A   15 MET cc_start: 0.8270 (mtp) cc_final: 0.8048 (mmt)
REVERT: A   48 ASN cc_start: 0.8318 (t0) cc_final: 0.7605 (t0)
REVERT: A   82 LYS cc_start: 0.8828 (mttt) cc_final: 0.8212 (mmmt)
REVERT: A  112 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8748 (tt0)
REVERT: A  113 PRO cc_start: 0.8672 (Cg_exo) cc_final: 0.8341 (Cg_endo)
REVERT: B   46 TYR cc_start: 0.8886 (m-80) cc_final: 0.8605 (m-80)
REVERT: B  116 ASN cc_start: 0.9596 (t0) cc_final: 0.9140 (t0)
REVERT: B  189 ASN cc_start: 0.8897 (m-40) cc_final: 0.8301 (t0)
REVERT: B  206 VAL cc_start: 0.8842 (m) cc_final: 0.8489 (p)
REVERT: B  213 MET cc_start: 0.8741 (mmm) cc_final: 0.8431 (mmm)
REVERT: B  259 LYS cc_start: 0.9053 (mttt) cc_final: 0.7372 (pttm)
REVERT: B  321 ASP cc_start: 0.9021 (t0) cc_final: 0.8738 (t0)
REVERT: B  353 ASP cc_start: 0.8818 (t0) cc_final: 0.8355 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1226
  time to fit residues: 16.9122
Evaluate side-chains
  82 residues out of total 481 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 7 optimal weight:    9.9990
   chunk 37 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 1 optimal weight:    0.0050
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.6002

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

Flipped N/Q/H residues before XYZ refinement:
** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 GLN
** B 233 ASN ** 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 = 0.3060 r_free = 0.3060 target = 0.105985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.093610 restraints weight = 6809.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.095208 restraints weight = 4795.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.096378 restraints weight = 3687.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.6602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4463  Z= 0.210
  Angle     :  0.574   9.035   6074  Z= 0.295
  Chirality :  0.045   0.147    673
  Planarity :  0.004   0.047    782
  Dihedral  :  4.102  13.634    594
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.36), residues: 550
  helix: -1.23 (0.76), residues: 45
  sheet:  0.97 (0.39), residues: 195
  loop : -1.00 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 115 
 HIS   0.001   0.000   HIS A  71 
 PHE   0.019   0.002   PHE B  62 
 TYR   0.019   0.001   TYR B 278 
 ARG   0.004   0.000   ARG A  61 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1431.12 seconds
wall clock time: 26 minutes 38.07 seconds (1598.07 seconds total)