Starting phenix.real_space_refine
on Sat May 10 23:16:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9chx_45604/05_2025/9chx_45604.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9chx_45604/05_2025/9chx_45604.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9chx_45604/05_2025/9chx_45604.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9chx_45604/05_2025/9chx_45604.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9chx_45604/05_2025/9chx_45604.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9chx_45604/05_2025/9chx_45604.cif"
  }
  resolution = 3.5
  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=   0.010 sd=   0.075
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      48      5.16       5
     C    4644      2.51       5
     N    1164      2.21       5
     O    1273      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7129
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3450
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3450
          Classifications: {'peptide': 432}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 9, 'TRANS': 422}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 2792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 350, 2792
          Classifications: {'peptide': 350}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 20, 'TRANS': 329}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 41
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 44
    Chain: "C"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 808
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 7, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'GLU%COO:oxt': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'CAU': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 57
          Unusual residues: {'FK5': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.83, per 1000 atoms: 0.68
  Number of scatterers: 7129
  At special positions: 0
  Unit cell: (68.85, 84.15, 155.55, 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      48     16.00
     O    1273      8.00
     N    1164      7.00
     C    4644      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 106 " - pdb=" SG  CYS A 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 184 " - pdb=" SG  CYS A 190 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.89
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1668

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 4 sheets defined
      54.6% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 60
      removed outlier: 3.581A  pdb=" N   ILE A  58 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LYS A  60 " --> pdb=" O   THR A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 97
      Proline residue:  A  88  - end of helix
    Processing helix  chain 'A' and resid 103 through 137
      removed outlier: 3.907A  pdb=" N   GLU A 107 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   THR A 123 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU A 124 " --> pdb=" O   SER A 120 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE A 135 " --> pdb=" O   ARG A 131 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   SER A 137 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 145
    Processing helix  chain 'A' and resid 146 through 171
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 178 through 186
    Processing helix  chain 'A' and resid 196 through 208
    Processing helix  chain 'A' and resid 209 through 226
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 3.801A  pdb=" N   ALA A 232 " --> pdb=" O   GLN A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 246
    Processing helix  chain 'A' and resid 254 through 259
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 286 through 295
      removed outlier: 3.882A  pdb=" N   ILE A 291 " --> pdb=" O   PHE A 287 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   GLU A 292 " --> pdb=" O   LYS A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 315
      removed outlier: 3.928A  pdb=" N   LYS A 306 " --> pdb=" O   ASP A 302 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   TYR A 314 " --> pdb=" O   ALA A 310 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ASP A 315 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 336
      removed outlier: 3.791A  pdb=" N   LEU A 331 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   MET A 334 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY A 336 " --> pdb=" O   LYS A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 356
    Processing helix  chain 'A' and resid 364 through 372
    Processing helix  chain 'A' and resid 394 through 421
      Proline residue:  A 411  - end of helix
    Processing helix  chain 'A' and resid 429 through 444
      removed outlier: 4.127A  pdb=" N   ASN A 435 " --> pdb=" O   TYR A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 450
      removed outlier: 3.520A  pdb=" N   ILE A 448 " --> pdb=" O   PHE A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 463
      removed outlier: 3.800A  pdb=" N   ILE A 457 " --> pdb=" O   PRO A 453 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ALA A 458 " --> pdb=" O   ASP A 454 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   LEU A 462 " --> pdb=" O   ALA A 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 50
    Processing helix  chain 'B' and resid 56 through 73
      removed outlier: 4.028A  pdb=" N   GLN B  73 " --> pdb=" O   SER B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 105
    Processing helix  chain 'B' and resid 124 through 139
    Processing helix  chain 'B' and resid 152 through 159
      removed outlier: 3.577A  pdb=" N   THR B 156 " --> pdb=" O   CYS B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 169
    Processing helix  chain 'B' and resid 170 through 182
      removed outlier: 3.695A  pdb=" N   TYR B 174 " --> pdb=" O   SER B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 212
    Processing helix  chain 'B' and resid 224 through 230
      removed outlier: 3.709A  pdb=" N   LEU B 230 " --> pdb=" O   MET B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 271
    Processing helix  chain 'B' and resid 309 through 313
    Processing helix  chain 'B' and resid 342 through 346
      removed outlier: 3.779A  pdb=" N   MET B 346 " --> pdb=" O   PRO B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 353
    Processing helix  chain 'B' and resid 353 through 369
      removed outlier: 3.514A  pdb=" N   GLU B 358 " --> pdb=" O   PRO B 354 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   LYS B 359 " --> pdb=" O   PHE B 355 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 64
      removed outlier: 3.965A  pdb=" N   ALA C  64 " --> pdb=" O   GLU C  60 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 79 through 80
      removed outlier: 3.502A  pdb=" N   ILE B  80 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ILE B 276 " --> pdb=" O   ILE B 302 " (cutoff:3.500A)
      removed outlier: 7.906A  pdb=" N   ILE B 304 " --> pdb=" O   ILE B 276 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   ARG B 278 " --> pdb=" O   ILE B 304 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 143 through 145
    Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 8
      removed outlier: 6.984A  pdb=" N   VAL C   4 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 7.971A  pdb=" N   THR C  75 " --> pdb=" O   VAL C   4 " (cutoff:3.500A)
      removed outlier: 5.506A  pdb=" N   THR C   6 " --> pdb=" O   LYS C  73 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   LYS C  73 " --> pdb=" O   THR C   6 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL C  98 " --> pdb=" O   MET C  29 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 49
      removed outlier: 6.237A  pdb=" N   HIS C  25 " --> pdb=" O   LEU C 103 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   LEU C 103 " --> pdb=" O   HIS C  25 " (cutoff:3.500A)

    340 hydrogen bonds defined for protein.
    978 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: 1.84

  Time building geometry restraints manager: 2.14 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2232
        1.34 -     1.46: 1723
        1.46 -     1.58: 3277
        1.58 -     1.70: 0
        1.70 -     1.82: 73
  Bond restraints: 7305
  Sorted by residual:
  bond pdb=" C9  FK5 C 201 "
       pdb=" O4  FK5 C 201 "
    ideal  model  delta    sigma   weight residual
    1.206  1.409 -0.203 2.00e-02 2.50e+03 1.03e+02
  bond pdb=" C1  FK5 C 201 "
       pdb=" O2  FK5 C 201 "
    ideal  model  delta    sigma   weight residual
    1.211  1.407 -0.196 2.00e-02 2.50e+03 9.65e+01
  bond pdb=" C22 FK5 C 201 "
       pdb=" O9  FK5 C 201 "
    ideal  model  delta    sigma   weight residual
    1.215  1.407 -0.192 2.00e-02 2.50e+03 9.22e+01
  bond pdb=" C8  FK5 C 201 "
       pdb=" O3  FK5 C 201 "
    ideal  model  delta    sigma   weight residual
    1.232  1.410 -0.178 2.00e-02 2.50e+03 7.94e+01
  bond pdb=" C8  FK5 C 201 "
       pdb=" C9  FK5 C 201 "
    ideal  model  delta    sigma   weight residual
    1.537  1.396  0.141 2.00e-02 2.50e+03 4.95e+01
  ... (remaining 7300 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 9701
        2.00 -     3.99: 169
        3.99 -     5.99: 30
        5.99 -     7.99: 8
        7.99 -     9.98: 4
  Bond angle restraints: 9912
  Sorted by residual:
  angle pdb=" N   GLN B 193 "
        pdb=" CA  GLN B 193 "
        pdb=" C   GLN B 193 "
      ideal   model   delta    sigma   weight residual
     114.56  110.40    4.16 1.27e+00 6.20e-01 1.07e+01
  angle pdb=" C2  FK5 C 201 "
        pdb=" C1  FK5 C 201 "
        pdb=" O1  FK5 C 201 "
      ideal   model   delta    sigma   weight residual
     112.57  122.39   -9.82 3.00e+00 1.11e-01 1.07e+01
  angle pdb=" C27 FK5 C 201 "
        pdb=" C28 FK5 C 201 "
        pdb=" C29 FK5 C 201 "
      ideal   model   delta    sigma   weight residual
     127.93  119.24    8.69 3.00e+00 1.11e-01 8.39e+00
  angle pdb=" CA  LEU B 364 "
        pdb=" CB  LEU B 364 "
        pdb=" CG  LEU B 364 "
      ideal   model   delta    sigma   weight residual
     116.30  106.32    9.98 3.50e+00 8.16e-02 8.14e+00
  angle pdb=" C   VAL A 206 "
        pdb=" CA  VAL A 206 "
        pdb=" CB  VAL A 206 "
      ideal   model   delta    sigma   weight residual
     111.20  107.89    3.31 1.24e+00 6.50e-01 7.13e+00
  ... (remaining 9907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.74: 4283
       35.74 -    71.49: 81
       71.49 -   107.23: 9
      107.23 -   142.97: 2
      142.97 -   178.72: 6
  Dihedral angle restraints: 4381
    sinusoidal: 1795
      harmonic: 2586
  Sorted by residual:
  dihedral pdb=" C13 FK5 C 201 "
           pdb=" C14 FK5 C 201 "
           pdb=" C15 FK5 C 201 "
           pdb=" O8  FK5 C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     108.57  -72.71 -178.72     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" O5  FK5 C 201 "
           pdb=" C14 FK5 C 201 "
           pdb=" C15 FK5 C 201 "
           pdb=" O8  FK5 C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -11.37  167.10 -178.47     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C13 FK5 C 201 "
           pdb=" C14 FK5 C 201 "
           pdb=" C15 FK5 C 201 "
           pdb=" C16 FK5 C 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -123.85   48.96 -172.81     1      3.00e+01 1.11e-03 2.12e+01
  ... (remaining 4378 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 785
       0.043 -    0.086: 268
       0.086 -    0.129: 51
       0.129 -    0.172: 9
       0.172 -    0.215: 3
  Chirality restraints: 1116
  Sorted by residual:
  chirality pdb=" C10 FK5 C 201 "
            pdb=" C11 FK5 C 201 "
            pdb=" C9  FK5 C 201 "
            pdb=" O5  FK5 C 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.69    2.47    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" C26 FK5 C 201 "
            pdb=" C25 FK5 C 201 "
            pdb=" C27 FK5 C 201 "
            pdb=" O1  FK5 C 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.61   -2.40   -0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" C16 CAU A 501 "
            pdb=" C15 CAU A 501 "
            pdb=" C18 CAU A 501 "
            pdb=" O17 CAU A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.31    2.49   -0.19 2.00e-01 2.50e+01 8.90e-01
  ... (remaining 1113 not shown)

  Planarity restraints: 1247
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C26 FK5 C 201 "   -0.126 2.00e-02 2.50e+03   1.35e-01 2.29e+02
        pdb=" C27 FK5 C 201 "    0.052 2.00e-02 2.50e+03
        pdb=" C28 FK5 C 201 "    0.208 2.00e-02 2.50e+03
        pdb=" C29 FK5 C 201 "   -0.169 2.00e-02 2.50e+03
        pdb=" C42 FK5 C 201 "    0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C18 FK5 C 201 "   -0.075 2.00e-02 2.50e+03   8.33e-02 8.68e+01
        pdb=" C19 FK5 C 201 "    0.023 2.00e-02 2.50e+03
        pdb=" C20 FK5 C 201 "    0.133 2.00e-02 2.50e+03
        pdb=" C21 FK5 C 201 "   -0.103 2.00e-02 2.50e+03
        pdb=" C37 FK5 C 201 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  77 "    0.030 5.00e-02 4.00e+02   4.59e-02 3.37e+00
        pdb=" N   PRO C  78 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO C  78 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C  78 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1244 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 145
        2.70 -     3.25: 7080
        3.25 -     3.80: 10807
        3.80 -     4.35: 13634
        4.35 -     4.90: 23055
  Nonbonded interactions: 54721
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 293 "
            pdb=" O   PHE B 298 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" OG  SER A 323 "
            pdb=" O   THR B  13 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" OG1 THR C   6 "
            pdb=" OE1 GLN C  70 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OH  TYR C  82 "
            pdb=" O3  FK5 C 201 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OD1 ASP A 231 "
            pdb=" NZ  LYS A 236 "
     model   vdw
     2.313 3.120
  ... (remaining 54716 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
========== 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:             1.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     19.690
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6540
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      :  0.007   0.203   7307  Z= 0.333
  Angle     :  0.698   9.985   9916  Z= 0.356
  Chirality :  0.045   0.215   1116
  Planarity :  0.006   0.135   1247
  Dihedral  : 17.123 178.718   2707
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.53 (0.29), residues: 879
  helix:  0.33 (0.25), residues: 444
  sheet: -0.36 (0.60), residues: 74
  loop : -1.13 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 109 
 HIS   0.011   0.001   HIS B 280 
 PHE   0.019   0.002   PHE A 223 
 TYR   0.012   0.001   TYR B 259 
 ARG   0.002   0.000   ARG A 272 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14086 (  340)
  hydrogen bonds       : angle       5.60741 (  978)
  SS BOND              : bond        0.00155 (    2)
  SS BOND              : angle       0.62589 (    4)
  covalent geometry    : bond        0.00686 ( 7305)
  covalent geometry    : angle       0.69788 ( 9912)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
REVERT: C  100 ASP cc_start: 0.7046 (t70) cc_final: 0.6704 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1587
  time to fit residues: 24.1296
Evaluate side-chains
  79 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0070
   chunk 68 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.4006

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

Flipped N/Q/H residues before XYZ refinement:
A 197 GLN
A 435 ASN
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 332 GLN
C  94 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.198493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.157737 restraints weight = 8210.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.159061 restraints weight = 7255.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.161743 restraints weight = 6126.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6836
moved from start:          0.1167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7307  Z= 0.181
  Angle     :  0.625  11.451   9916  Z= 0.326
  Chirality :  0.044   0.160   1116
  Planarity :  0.005   0.076   1247
  Dihedral  : 15.585 174.752   1066
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 10.88 %
    Favored  : 87.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.49 (0.29), residues: 879
  helix:  0.40 (0.25), residues: 449
  sheet: -1.10 (0.59), residues: 70
  loop : -0.98 (0.35), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 109 
 HIS   0.007   0.001   HIS B 280 
 PHE   0.019   0.002   PHE A 242 
 TYR   0.027   0.002   TYR B 174 
 ARG   0.002   0.000   ARG A 272 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04721 (  340)
  hydrogen bonds       : angle       4.63919 (  978)
  SS BOND              : bond        0.00307 (    2)
  SS BOND              : angle       0.99277 (    4)
  covalent geometry    : bond        0.00427 ( 7305)
  covalent geometry    : angle       0.62461 ( 9912)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
REVERT: C  100 ASP cc_start: 0.7346 (t70) cc_final: 0.6877 (t0)
  outliers start: 12
  outliers final: 9
  residues processed: 81
  average time/residue: 0.1611
  time to fit residues: 19.1165
Evaluate side-chains
  83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain B residue  284 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 34 optimal weight:    0.2980
   chunk 3 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.198475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.157172 restraints weight = 8295.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.157196 restraints weight = 7274.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.159939 restraints weight = 5893.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.4081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6775
moved from start:          0.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7307  Z= 0.142
  Angle     :  0.569   9.890   9916  Z= 0.296
  Chirality :  0.042   0.133   1116
  Planarity :  0.004   0.059   1247
  Dihedral  : 14.880 173.784   1066
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 15.33 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.36 (0.29), residues: 879
  helix:  0.52 (0.25), residues: 448
  sheet: -1.18 (0.58), residues: 70
  loop : -0.91 (0.35), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 109 
 HIS   0.004   0.001   HIS B 280 
 PHE   0.016   0.001   PHE A 242 
 TYR   0.017   0.001   TYR B 139 
 ARG   0.002   0.000   ARG B 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04156 (  340)
  hydrogen bonds       : angle       4.39967 (  978)
  SS BOND              : bond        0.00478 (    2)
  SS BOND              : angle       1.49808 (    4)
  covalent geometry    : bond        0.00328 ( 7305)
  covalent geometry    : angle       0.56881 ( 9912)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.756 
Fit side-chains
REVERT: A  179 GLN cc_start: 0.8802 (pm20) cc_final: 0.8552 (tp-100)
REVERT: B  322 LYS cc_start: 0.7868 (mttm) cc_final: 0.7564 (mttm)
REVERT: C  100 ASP cc_start: 0.7331 (t70) cc_final: 0.6781 (t0)
  outliers start: 16
  outliers final: 11
  residues processed: 89
  average time/residue: 0.1536
  time to fit residues: 19.9207
Evaluate side-chains
  91 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  191 CYS
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain B residue  280 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 39 optimal weight:    9.9990
   chunk 74 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 79 optimal weight:    9.9990
   chunk 65 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 392 HIS
** A 441 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 = 0.4417 r_free = 0.4417 target = 0.195391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.154240 restraints weight = 8411.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.154241 restraints weight = 7440.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.156916 restraints weight = 6002.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6815
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   7307  Z= 0.172
  Angle     :  0.665  15.139   9916  Z= 0.339
  Chirality :  0.044   0.229   1116
  Planarity :  0.004   0.055   1247
  Dihedral  : 14.614 173.398   1066
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.82 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -0.42 (0.29), residues: 879
  helix:  0.51 (0.25), residues: 441
  sheet: -1.31 (0.57), residues: 70
  loop : -0.95 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 109 
 HIS   0.004   0.001   HIS B 280 
 PHE   0.014   0.002   PHE A 290 
 TYR   0.015   0.001   TYR B 139 
 ARG   0.002   0.000   ARG B 291 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04309 (  340)
  hydrogen bonds       : angle       4.47607 (  978)
  SS BOND              : bond        0.00899 (    2)
  SS BOND              : angle       8.86334 (    4)
  covalent geometry    : bond        0.00417 ( 7305)
  covalent geometry    : angle       0.64066 ( 9912)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.800 
Fit side-chains
REVERT: B   73 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7307 (pm20)
REVERT: B  322 LYS cc_start: 0.7847 (mttm) cc_final: 0.7545 (mttm)
REVERT: C  100 ASP cc_start: 0.7322 (t70) cc_final: 0.6739 (t0)
  outliers start: 18
  outliers final: 11
  residues processed: 91
  average time/residue: 0.1609
  time to fit residues: 21.0367
Evaluate side-chains
  87 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  191 CYS
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  226 MET
Chi-restraints excluded: chain B residue  280 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 73 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0170
   chunk 8 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 31 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.199886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.159090 restraints weight = 8255.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.161464 restraints weight = 6370.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.163562 restraints weight = 5528.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.4122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6745
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7307  Z= 0.119
  Angle     :  0.581   9.407   9916  Z= 0.300
  Chirality :  0.041   0.169   1116
  Planarity :  0.004   0.048   1247
  Dihedral  : 14.031 172.662   1066
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 19.00 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.29), residues: 879
  helix:  0.74 (0.26), residues: 443
  sheet: -1.28 (0.57), residues: 70
  loop : -0.88 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 109 
 HIS   0.003   0.001   HIS B 280 
 PHE   0.015   0.001   PHE A 242 
 TYR   0.017   0.001   TYR B 174 
 ARG   0.002   0.000   ARG B 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03657 (  340)
  hydrogen bonds       : angle       4.24757 (  978)
  SS BOND              : bond        0.00530 (    2)
  SS BOND              : angle       5.77912 (    4)
  covalent geometry    : bond        0.00269 ( 7305)
  covalent geometry    : angle       0.56899 ( 9912)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.795 
Fit side-chains
REVERT: A  145 LEU cc_start: 0.4219 (OUTLIER) cc_final: 0.3981 (tt)
REVERT: B   73 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7312 (pm20)
REVERT: B  174 TYR cc_start: 0.7270 (OUTLIER) cc_final: 0.7020 (t80)
REVERT: B  322 LYS cc_start: 0.7872 (mttm) cc_final: 0.7555 (mttm)
REVERT: C  100 ASP cc_start: 0.7303 (t70) cc_final: 0.6755 (t0)
  outliers start: 19
  outliers final: 12
  residues processed: 95
  average time/residue: 0.1509
  time to fit residues: 20.7447
Evaluate side-chains
  91 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  280 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 67 optimal weight:    0.5980
   chunk 15 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0970
   chunk 83 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 17 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.203595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.162982 restraints weight = 8225.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.164902 restraints weight = 6412.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.167767 restraints weight = 5264.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.4174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6724
moved from start:          0.1886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7307  Z= 0.111
  Angle     :  0.559   8.647   9916  Z= 0.287
  Chirality :  0.041   0.155   1116
  Planarity :  0.004   0.048   1247
  Dihedral  : 13.544 171.843   1066
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.27 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.18 (0.29), residues: 879
  helix:  0.72 (0.26), residues: 452
  sheet: -1.28 (0.57), residues: 70
  loop : -0.88 (0.35), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A  99 
 HIS   0.003   0.001   HIS B 280 
 PHE   0.013   0.001   PHE A 242 
 TYR   0.014   0.001   TYR B 174 
 ARG   0.002   0.000   ARG B 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03478 (  340)
  hydrogen bonds       : angle       4.14179 (  978)
  SS BOND              : bond        0.00386 (    2)
  SS BOND              : angle       5.42423 (    4)
  covalent geometry    : bond        0.00245 ( 7305)
  covalent geometry    : angle       0.54811 ( 9912)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A  145 LEU cc_start: 0.4189 (OUTLIER) cc_final: 0.3958 (tt)
REVERT: B   73 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7281 (pm20)
REVERT: B  223 TYR cc_start: 0.7365 (p90) cc_final: 0.7130 (p90)
REVERT: B  281 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7414 (mm-30)
REVERT: B  322 LYS cc_start: 0.7868 (mttm) cc_final: 0.7546 (mttm)
REVERT: C   30 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6834 (mp)
REVERT: C  100 ASP cc_start: 0.7305 (t70) cc_final: 0.6739 (t0)
  outliers start: 22
  outliers final: 14
  residues processed: 101
  average time/residue: 0.1522
  time to fit residues: 22.3825
Evaluate side-chains
  96 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   99 TRP
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain C residue   30 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 18 optimal weight:    0.5980
   chunk 71 optimal weight:    0.3980
   chunk 41 optimal weight:    0.8980
   chunk 68 optimal weight:    7.9990
   chunk 59 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   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 441 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.203482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.167089 restraints weight = 8657.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.167503 restraints weight = 9774.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.169743 restraints weight = 8812.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.4262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7307  Z= 0.116
  Angle     :  0.561   8.771   9916  Z= 0.289
  Chirality :  0.041   0.132   1116
  Planarity :  0.004   0.066   1247
  Dihedral  : 13.305 172.267   1066
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 20.05 %
    Favored  : 77.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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: -0.05 (0.30), residues: 879
  helix:  0.80 (0.26), residues: 449
  sheet: -0.95 (0.56), residues: 80
  loop : -0.81 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A  99 
 HIS   0.004   0.001   HIS B 280 
 PHE   0.013   0.001   PHE A 290 
 TYR   0.013   0.001   TYR B 174 
 ARG   0.002   0.000   ARG B 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03549 (  340)
  hydrogen bonds       : angle       4.11626 (  978)
  SS BOND              : bond        0.00274 (    2)
  SS BOND              : angle       4.42306 (    4)
  covalent geometry    : bond        0.00261 ( 7305)
  covalent geometry    : angle       0.55420 ( 9912)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.869 
Fit side-chains
REVERT: A  145 LEU cc_start: 0.4708 (OUTLIER) cc_final: 0.4462 (tt)
REVERT: A  362 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6630 (mtp85)
REVERT: B   73 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7528 (pm20)
REVERT: B   98 MET cc_start: 0.5978 (mmt) cc_final: 0.5307 (mmt)
REVERT: B  322 LYS cc_start: 0.7969 (mttm) cc_final: 0.7705 (mttm)
REVERT: C  100 ASP cc_start: 0.7362 (t70) cc_final: 0.6893 (t0)
  outliers start: 21
  outliers final: 14
  residues processed: 99
  average time/residue: 0.1740
  time to fit residues: 24.4492
Evaluate side-chains
  95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   99 TRP
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  362 ARG
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  367 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 65 optimal weight:    0.4980
   chunk 27 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0570
   chunk 48 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 74 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.6298

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.203588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.167705 restraints weight = 8639.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.169180 restraints weight = 9158.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.171161 restraints weight = 7514.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.4274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6926
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7307  Z= 0.116
  Angle     :  0.563   9.722   9916  Z= 0.288
  Chirality :  0.041   0.224   1116
  Planarity :  0.004   0.055   1247
  Dihedral  : 13.356 173.004   1066
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 20.05 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -0.05 (0.30), residues: 879
  helix:  0.80 (0.26), residues: 449
  sheet: -1.04 (0.54), residues: 83
  loop : -0.77 (0.35), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A  99 
 HIS   0.004   0.001   HIS B 280 
 PHE   0.012   0.001   PHE A 290 
 TYR   0.014   0.001   TYR B 139 
 ARG   0.002   0.000   ARG B 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03553 (  340)
  hydrogen bonds       : angle       4.07705 (  978)
  SS BOND              : bond        0.01545 (    2)
  SS BOND              : angle       2.54631 (    4)
  covalent geometry    : bond        0.00261 ( 7305)
  covalent geometry    : angle       0.56072 ( 9912)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 78
  time to evaluate  : 0.817 
Fit side-chains
REVERT: A  145 LEU cc_start: 0.4633 (OUTLIER) cc_final: 0.4425 (tt)
REVERT: A  362 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6616 (mtp85)
REVERT: B   73 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7517 (pm20)
REVERT: B   98 MET cc_start: 0.6007 (mmt) cc_final: 0.5383 (mmt)
REVERT: B  137 ILE cc_start: 0.5414 (mt) cc_final: 0.5213 (mt)
REVERT: B  276 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7800 (mm)
REVERT: C  100 ASP cc_start: 0.7370 (t70) cc_final: 0.6891 (t0)
  outliers start: 26
  outliers final: 17
  residues processed: 99
  average time/residue: 0.1693
  time to fit residues: 23.8383
Evaluate side-chains
  98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   99 TRP
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  362 ARG
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  444 PHE
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  367 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 25 optimal weight:    0.1980
   chunk 14 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 28 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.201430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.164925 restraints weight = 8693.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.164410 restraints weight = 10423.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.167205 restraints weight = 8860.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.4235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7307  Z= 0.136
  Angle     :  0.593  10.489   9916  Z= 0.302
  Chirality :  0.042   0.180   1116
  Planarity :  0.004   0.052   1247
  Dihedral  : 13.445 174.379   1066
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 20.05 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -0.14 (0.29), residues: 879
  helix:  0.70 (0.26), residues: 449
  sheet: -1.02 (0.56), residues: 80
  loop : -0.80 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A  99 
 HIS   0.004   0.001   HIS B 280 
 PHE   0.014   0.001   PHE A 290 
 TYR   0.015   0.001   TYR B 174 
 ARG   0.002   0.000   ARG B 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03842 (  340)
  hydrogen bonds       : angle       4.16441 (  978)
  SS BOND              : bond        0.00948 (    2)
  SS BOND              : angle       2.27179 (    4)
  covalent geometry    : bond        0.00316 ( 7305)
  covalent geometry    : angle       0.59112 ( 9912)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 78
  time to evaluate  : 0.754 
Fit side-chains
REVERT: A  362 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.6607 (mtp85)
REVERT: B   73 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7487 (pm20)
REVERT: B   98 MET cc_start: 0.6110 (mmt) cc_final: 0.5492 (mmt)
REVERT: B  276 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7827 (mm)
REVERT: C  100 ASP cc_start: 0.7401 (t70) cc_final: 0.6908 (t0)
  outliers start: 25
  outliers final: 18
  residues processed: 96
  average time/residue: 0.1663
  time to fit residues: 22.5958
Evaluate side-chains
  96 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   99 TRP
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  362 ARG
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  444 PHE
Chi-restraints excluded: chain B residue   73 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  289 MET
Chi-restraints excluded: chain B residue  367 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 60 optimal weight:    0.1980
   chunk 76 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 49 optimal weight:    0.1980
   chunk 54 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.206247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.169493 restraints weight = 8774.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.170638 restraints weight = 9409.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.172866 restraints weight = 7695.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.4299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6891
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   7307  Z= 0.110
  Angle     :  0.557   8.987   9916  Z= 0.282
  Chirality :  0.040   0.162   1116
  Planarity :  0.004   0.048   1247
  Dihedral  : 13.329 173.824   1066
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.45 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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: -0.02 (0.30), residues: 879
  helix:  0.83 (0.26), residues: 448
  sheet: -1.05 (0.54), residues: 83
  loop : -0.75 (0.36), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A  99 
 HIS   0.003   0.001   HIS B 280 
 PHE   0.012   0.001   PHE A 297 
 TYR   0.018   0.001   TYR B 174 
 ARG   0.002   0.000   ARG B 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03556 (  340)
  hydrogen bonds       : angle       4.04858 (  978)
  SS BOND              : bond        0.00839 (    2)
  SS BOND              : angle       1.99986 (    4)
  covalent geometry    : bond        0.00241 ( 7305)
  covalent geometry    : angle       0.55594 ( 9912)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.729 
Fit side-chains
REVERT: A  362 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6549 (mtp85)
REVERT: B   98 MET cc_start: 0.6063 (mmt) cc_final: 0.5465 (mmt)
REVERT: B  276 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7746 (mm)
REVERT: C  100 ASP cc_start: 0.7369 (t70) cc_final: 0.6893 (t0)
  outliers start: 22
  outliers final: 16
  residues processed: 98
  average time/residue: 0.1604
  time to fit residues: 22.5273
Evaluate side-chains
  92 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   99 TRP
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  184 CYS
Chi-restraints excluded: chain A residue  190 CYS
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  225 GLU
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  362 ARG
Chi-restraints excluded: chain A residue  369 CYS
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  444 PHE
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  276 ILE
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  367 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 50 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 70 optimal weight:    0.2980
   chunk 2 optimal weight:    0.2980
   chunk 71 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 51 optimal weight:    0.5980
   chunk 84 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A  65 GLN
A 338 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.204297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.168331 restraints weight = 8661.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.171208 restraints weight = 9261.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.173262 restraints weight = 7807.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.4289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6892
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   7307  Z= 0.110
  Angle     :  0.563  10.780   9916  Z= 0.284
  Chirality :  0.040   0.150   1116
  Planarity :  0.004   0.048   1247
  Dihedral  : 13.315 174.289   1066
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 20.71 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

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:  0.03 (0.30), residues: 879
  helix:  0.88 (0.26), residues: 448
  sheet: -1.04 (0.54), residues: 83
  loop : -0.73 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  99 
 HIS   0.003   0.001   HIS B 280 
 PHE   0.023   0.001   PHE A 297 
 TYR   0.018   0.001   TYR B 174 
 ARG   0.002   0.000   ARG B 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03507 (  340)
  hydrogen bonds       : angle       4.00583 (  978)
  SS BOND              : bond        0.00738 (    2)
  SS BOND              : angle       1.86561 (    4)
  covalent geometry    : bond        0.00244 ( 7305)
  covalent geometry    : angle       0.56196 ( 9912)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2307.40 seconds
wall clock time: 41 minutes 8.05 seconds (2468.05 seconds total)