Starting phenix.real_space_refine
on Tue Feb 11 16:28:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p54_13194/02_2025/7p54_13194.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p54_13194/02_2025/7p54_13194.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p54_13194/02_2025/7p54_13194.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p54_13194/02_2025/7p54_13194.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p54_13194/02_2025/7p54_13194.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p54_13194/02_2025/7p54_13194.cif"
  }
  resolution = 3.3
  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=   0.000 sd=   0.004
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      50      5.16       5
     C    4030      2.51       5
     N     986      2.21       5
     O    1182      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6248
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3040
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 397, 3040
          Classifications: {'peptide': 397}
          Link IDs: {'PTRANS': 9, 'TRANS': 387}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3040
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 397, 3040
          Classifications: {'peptide': 397}
          Link IDs: {'PTRANS': 9, 'TRANS': 387}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.34, per 1000 atoms: 0.69
  Number of scatterers: 6248
  At special positions: 0
  Unit cell: (93.744, 70.308, 128.898, 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      50     16.00
     O    1182      8.00
     N     986      7.00
     C    4030      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 274 " - pdb=" SG  CYS A 382 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 300 " - pdb=" SG  CYS A 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 274 " - pdb=" SG  CYS B 382 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 300 " - pdb=" SG  CYS B 367 " 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
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A 601 " - " ASN A 283 "
      " NAG A 602 " - " ASN A  31 "
      " NAG B 601 " - " ASN B 283 "
      " NAG B 602 " - " ASN B  31 "
      " NAG C   1 " - " ASN A 352 "
      " NAG D   1 " - " ASN A 129 "
      " NAG E   1 " - " ASN B 352 "
      " NAG F   1 " - " ASN B 129 "
  Time building additional restraints: 1.95
  Conformation dependent library (CDL) restraints added in 926.3 milliseconds
  

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1480

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 0 sheets defined
      89.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 19
    Processing helix  chain 'A' and resid 38 through 72
    Processing helix  chain 'A' and resid 89 through 161
      removed outlier: 4.269A  pdb=" N   LEU A 150 " --> pdb=" O   MET A 146 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   GLU A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ILE A 160 " --> pdb=" O   ARG A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 187
      removed outlier: 3.744A  pdb=" N   LEU A 171 " --> pdb=" O   TYR A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 237
    Processing helix  chain 'A' and resid 238 through 276
      removed outlier: 3.560A  pdb=" N   SER A 244 " --> pdb=" O   CYS A 240 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ALA A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 285
    Processing helix  chain 'A' and resid 290 through 299
    Processing helix  chain 'A' and resid 308 through 337
      removed outlier: 3.580A  pdb=" N   VAL A 334 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
      Proline residue:  A 335  - end of helix
    Processing helix  chain 'A' and resid 341 through 365
    Processing helix  chain 'A' and resid 366 through 383
      removed outlier: 4.482A  pdb=" N   LEU A 370 " --> pdb=" O   ASP A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 409
    Processing helix  chain 'A' and resid 409 through 416
      removed outlier: 3.614A  pdb=" N   ALA A 413 " --> pdb=" O   ALA A 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 19
    Processing helix  chain 'B' and resid 38 through 72
    Processing helix  chain 'B' and resid 89 through 161
      removed outlier: 4.283A  pdb=" N   LEU B 150 " --> pdb=" O   MET B 146 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   GLU B 159 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ILE B 160 " --> pdb=" O   ARG B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 187
      removed outlier: 3.773A  pdb=" N   LEU B 171 " --> pdb=" O   TYR B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 237
    Processing helix  chain 'B' and resid 239 through 276
      removed outlier: 4.272A  pdb=" N   ALA B 276 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 285
    Processing helix  chain 'B' and resid 290 through 300
    Processing helix  chain 'B' and resid 308 through 337
      removed outlier: 3.597A  pdb=" N   VAL B 334 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
      Proline residue:  B 335  - end of helix
    Processing helix  chain 'B' and resid 340 through 365
      removed outlier: 3.772A  pdb=" N   LEU B 344 " --> pdb=" O   ALA B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 383
      removed outlier: 4.559A  pdb=" N   LEU B 370 " --> pdb=" O   ASP B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 409
    Processing helix  chain 'B' and resid 409 through 416
      removed outlier: 3.647A  pdb=" N   ALA B 413 " --> pdb=" O   ALA B 409 " (cutoff:3.500A)

    581 hydrogen bonds defined for protein.
    1743 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: 1.83

  Time building geometry restraints manager: 2.22 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: 1935
        1.34 -     1.46: 1538
        1.46 -     1.58: 2839
        1.58 -     1.70: 0
        1.70 -     1.82: 66
  Bond restraints: 6378
  Sorted by residual:
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.444 -0.038 2.00e-02 2.50e+03 3.53e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.443 -0.037 2.00e-02 2.50e+03 3.43e+00
  bond pdb=" C1  NAG B 602 "
       pdb=" O5  NAG B 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.33e+00
  bond pdb=" C1  NAG A 602 "
       pdb=" O5  NAG A 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.82e+00
  bond pdb=" C1  NAG B 601 "
       pdb=" O5  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.61e+00
  ... (remaining 6373 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 8390
        1.38 -     2.76: 254
        2.76 -     4.13: 34
        4.13 -     5.51: 11
        5.51 -     6.89: 3
  Bond angle restraints: 8692
  Sorted by residual:
  angle pdb=" C   VAL B  23 "
        pdb=" N   GLY B  24 "
        pdb=" CA  GLY B  24 "
      ideal   model   delta    sigma   weight residual
     121.44  117.03    4.41 1.45e+00 4.76e-01 9.25e+00
  angle pdb=" N   GLN A 325 "
        pdb=" CA  GLN A 325 "
        pdb=" CB  GLN A 325 "
      ideal   model   delta    sigma   weight residual
     110.16  114.31   -4.15 1.48e+00 4.57e-01 7.87e+00
  angle pdb=" N   ARG B 368 "
        pdb=" CA  ARG B 368 "
        pdb=" C   ARG B 368 "
      ideal   model   delta    sigma   weight residual
     111.11  114.34   -3.23 1.20e+00 6.94e-01 7.25e+00
  angle pdb=" N   GLY B  37 "
        pdb=" CA  GLY B  37 "
        pdb=" C   GLY B  37 "
      ideal   model   delta    sigma   weight residual
     114.25  111.02    3.23 1.30e+00 5.92e-01 6.18e+00
  angle pdb=" C   CYS B 367 "
        pdb=" N   ARG B 368 "
        pdb=" CA  ARG B 368 "
      ideal   model   delta    sigma   weight residual
     120.54  123.89   -3.35 1.35e+00 5.49e-01 6.16e+00
  ... (remaining 8687 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.06: 3460
       16.06 -    32.12: 290
       32.12 -    48.18: 91
       48.18 -    64.23: 25
       64.23 -    80.29: 8
  Dihedral angle restraints: 3874
    sinusoidal: 1570
      harmonic: 2304
  Sorted by residual:
  dihedral pdb=" CB  CYS A 300 "
           pdb=" SG  CYS A 300 "
           pdb=" SG  CYS A 367 "
           pdb=" CB  CYS A 367 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -162.49   76.49     1      1.00e+01 1.00e-02 7.36e+01
  dihedral pdb=" CB  CYS B 300 "
           pdb=" SG  CYS B 300 "
           pdb=" SG  CYS B 367 "
           pdb=" CB  CYS B 367 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -141.61   55.61     1      1.00e+01 1.00e-02 4.18e+01
  dihedral pdb=" CB  CYS A 274 "
           pdb=" SG  CYS A 274 "
           pdb=" SG  CYS A 382 "
           pdb=" CB  CYS A 382 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  128.88  -35.88     1      1.00e+01 1.00e-02 1.82e+01
  ... (remaining 3871 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 985
       0.063 -    0.126: 84
       0.126 -    0.188: 1
       0.188 -    0.251: 0
       0.251 -    0.314: 2
  Chirality restraints: 1072
  Sorted by residual:
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN B 129 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.09   -0.31 2.00e-01 2.50e+01 2.46e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 129 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" CA  GLN A 325 "
            pdb=" N   GLN A 325 "
            pdb=" C   GLN A 325 "
            pdb=" CB  GLN A 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.29e-01
  ... (remaining 1069 not shown)

  Planarity restraints: 1066
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  20 "   -0.055 5.00e-02 4.00e+02   8.28e-02 1.10e+01
        pdb=" N   PRO A  21 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO A  21 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A  21 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  20 "   -0.053 5.00e-02 4.00e+02   8.04e-02 1.03e+01
        pdb=" N   PRO B  21 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO B  21 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO B  21 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 147 "   -0.008 2.00e-02 2.50e+03   1.63e-02 2.66e+00
        pdb=" C   LYS B 147 "    0.028 2.00e-02 2.50e+03
        pdb=" O   LYS B 147 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   VAL B 148 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1063 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 737
        2.74 -     3.28: 6440
        3.28 -     3.82: 11254
        3.82 -     4.36: 11217
        4.36 -     4.90: 20634
  Nonbonded interactions: 50282
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 278 "
            pdb=" OH  TYR A 374 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OD1 ASN B 111 "
            pdb=" NH1 ARG B 212 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" OD2 ASP A  38 "
            pdb=" OG  SER A  40 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   ILE B 281 "
            pdb=" OG1 THR B 285 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" OD1 ASN A 111 "
            pdb=" NH1 ARG A 212 "
     model   vdw
     2.243 3.120
  ... (remaining 50277 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.210
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  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:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6378  Z= 0.234
  Angle     :  0.553   6.891   8692  Z= 0.294
  Chirality :  0.038   0.314   1072
  Planarity :  0.005   0.083   1058
  Dihedral  : 13.935  80.293   2382
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  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:  4.08 (0.29), residues: 786
  helix:  3.32 (0.18), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.34 (0.49), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 213 
 HIS   0.002   0.001   HIS A  18 
 PHE   0.012   0.002   PHE B 395 
 TYR   0.010   0.001   TYR A   8 
 ARG   0.007   0.001   ARG B 192 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.606 
Fit side-chains
REVERT: A   16 TRP cc_start: 0.6870 (m100) cc_final: 0.6646 (m100)
REVERT: A  207 TYR cc_start: 0.7718 (t80) cc_final: 0.7392 (t80)
REVERT: A  213 TRP cc_start: 0.8415 (t60) cc_final: 0.7703 (t-100)
REVERT: A  245 MET cc_start: 0.6533 (mmp) cc_final: 0.6259 (mmp)
REVERT: A  353 SER cc_start: 0.8925 (t) cc_final: 0.8714 (t)
REVERT: B   12 TRP cc_start: 0.8176 (p-90) cc_final: 0.7966 (p-90)
REVERT: B  213 TRP cc_start: 0.8324 (t60) cc_final: 0.7643 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1841
  time to fit residues: 32.1404
Evaluate side-chains
  116 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 32 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  72 HIS
B  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.150981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.120878 restraints weight = 6858.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.34
r_work: 0.3260 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.0861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6378  Z= 0.207
  Angle     :  0.496   4.878   8692  Z= 0.258
  Chirality :  0.038   0.239   1072
  Planarity :  0.004   0.052   1058
  Dihedral  :  7.328  59.841   1096
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  8.03 %
    Favored  : 90.61 %
  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:  4.20 (0.29), residues: 786
  helix:  3.47 (0.18), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.79 (0.51), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  16 
 HIS   0.003   0.001   HIS A  22 
 PHE   0.017   0.002   PHE A  62 
 TYR   0.020   0.001   TYR B   8 
 ARG   0.005   0.001   ARG A 295 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 0.608 
Fit side-chains
REVERT: A  207 TYR cc_start: 0.8183 (t80) cc_final: 0.7777 (t80)
REVERT: A  213 TRP cc_start: 0.8560 (t60) cc_final: 0.7671 (t-100)
REVERT: A  332 PHE cc_start: 0.7909 (m-10) cc_final: 0.7691 (m-10)
REVERT: A  336 LEU cc_start: 0.8871 (mp) cc_final: 0.8651 (mp)
REVERT: B    8 TYR cc_start: 0.7727 (t80) cc_final: 0.7448 (t80)
REVERT: B   16 TRP cc_start: 0.8040 (m100) cc_final: 0.7822 (m100)
REVERT: B  213 TRP cc_start: 0.8558 (t60) cc_final: 0.7590 (t-100)
REVERT: B  283 ASN cc_start: 0.8218 (t0) cc_final: 0.7882 (t0)
REVERT: B  322 MET cc_start: 0.8415 (mtp) cc_final: 0.8058 (mtp)
  outliers start: 9
  outliers final: 6
  residues processed: 127
  average time/residue: 0.1895
  time to fit residues: 31.4372
Evaluate side-chains
  123 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 64 optimal weight:    0.3980
   chunk 16 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 68 optimal weight:    0.3980
   chunk 53 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3855 r_free = 0.3855 target = 0.158513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.129361 restraints weight = 6890.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.27
r_work: 0.3235 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.1053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6378  Z= 0.186
  Angle     :  0.480   6.690   8692  Z= 0.244
  Chirality :  0.038   0.241   1072
  Planarity :  0.004   0.042   1058
  Dihedral  :  6.761  57.923   1096
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 11.06 %
    Favored  : 87.42 %
  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:  4.25 (0.29), residues: 786
  helix:  3.53 (0.18), residues: 668
  sheet:  None (None), residues: 0
  loop : -2.06 (0.50), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  16 
 HIS   0.002   0.001   HIS A 371 
 PHE   0.021   0.002   PHE A  62 
 TYR   0.017   0.001   TYR A   8 
 ARG   0.004   0.000   ARG A  26 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 TYR cc_start: 0.8238 (t80) cc_final: 0.7816 (t80)
REVERT: A  213 TRP cc_start: 0.8548 (t60) cc_final: 0.7660 (t-100)
REVERT: A  245 MET cc_start: 0.6520 (mmp) cc_final: 0.6079 (mmp)
REVERT: A  332 PHE cc_start: 0.8054 (m-10) cc_final: 0.7697 (m-10)
REVERT: A  336 LEU cc_start: 0.8910 (mp) cc_final: 0.8703 (mp)
REVERT: B    8 TYR cc_start: 0.7474 (t80) cc_final: 0.7099 (t80)
REVERT: B   16 TRP cc_start: 0.7986 (m100) cc_final: 0.7774 (m100)
REVERT: B  213 TRP cc_start: 0.8543 (t60) cc_final: 0.7590 (t-100)
REVERT: B  283 ASN cc_start: 0.8341 (t0) cc_final: 0.8003 (t0)
  outliers start: 10
  outliers final: 9
  residues processed: 132
  average time/residue: 0.1919
  time to fit residues: 32.9886
Evaluate side-chains
  131 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 122
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    0.0030
   chunk 28 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 64 optimal weight:    0.5980
   chunk 77 optimal weight:    0.3980
   chunk 63 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.4790

-------------------------------------------------------------------------------
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 = 0.3858 r_free = 0.3858 target = 0.159063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.129386 restraints weight = 6951.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 2.32
r_work: 0.3309 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.1266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6378  Z= 0.159
  Angle     :  0.451   6.449   8692  Z= 0.234
  Chirality :  0.037   0.241   1072
  Planarity :  0.004   0.036   1058
  Dihedral  :  6.285  57.321   1096
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.09 %
    Favored  : 83.94 %
  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:  4.38 (0.29), residues: 786
  helix:  3.57 (0.18), residues: 678
  sheet:  None (None), residues: 0
  loop : -2.22 (0.52), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  16 
 HIS   0.002   0.001   HIS B  22 
 PHE   0.025   0.002   PHE A  62 
 TYR   0.016   0.001   TYR A   8 
 ARG   0.003   0.000   ARG A 295 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.734 
Fit side-chains
REVERT: A  166 ASP cc_start: 0.8540 (p0) cc_final: 0.8309 (p0)
REVERT: A  207 TYR cc_start: 0.8280 (t80) cc_final: 0.7860 (t80)
REVERT: A  213 TRP cc_start: 0.8492 (t60) cc_final: 0.7684 (t-100)
REVERT: A  245 MET cc_start: 0.6561 (mmp) cc_final: 0.5945 (mmp)
REVERT: A  283 ASN cc_start: 0.8097 (t0) cc_final: 0.7810 (t0)
REVERT: A  332 PHE cc_start: 0.8081 (m-10) cc_final: 0.7739 (m-10)
REVERT: A  336 LEU cc_start: 0.8872 (mp) cc_final: 0.8664 (mp)
REVERT: B    8 TYR cc_start: 0.7447 (t80) cc_final: 0.7130 (t80)
REVERT: B   16 TRP cc_start: 0.8015 (m100) cc_final: 0.7777 (m100)
REVERT: B  213 TRP cc_start: 0.8527 (t60) cc_final: 0.7629 (t-100)
REVERT: B  283 ASN cc_start: 0.8468 (t0) cc_final: 0.8129 (t0)
  outliers start: 13
  outliers final: 13
  residues processed: 135
  average time/residue: 0.1953
  time to fit residues: 34.1659
Evaluate side-chains
  136 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 46 optimal weight:    6.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3815 r_free = 0.3815 target = 0.155067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.125495 restraints weight = 7057.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.32
r_work: 0.3193 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.1345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6378  Z= 0.220
  Angle     :  0.495   7.120   8692  Z= 0.251
  Chirality :  0.038   0.236   1072
  Planarity :  0.004   0.033   1058
  Dihedral  :  6.047  56.819   1096
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.61 %
    Favored  : 81.52 %
  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:  4.26 (0.29), residues: 786
  helix:  3.41 (0.18), residues: 686
  sheet:  None (None), residues: 0
  loop : -2.18 (0.56), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  13 
 HIS   0.003   0.001   HIS A  22 
 PHE   0.027   0.002   PHE A  62 
 TYR   0.015   0.002   TYR A   8 
 ARG   0.003   0.001   ARG A 295 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.683 
Fit side-chains
REVERT: A  207 TYR cc_start: 0.8310 (t80) cc_final: 0.7835 (t80)
REVERT: A  213 TRP cc_start: 0.8588 (t60) cc_final: 0.7617 (t-100)
REVERT: A  245 MET cc_start: 0.6615 (mmp) cc_final: 0.6020 (mmp)
REVERT: A  283 ASN cc_start: 0.8118 (t0) cc_final: 0.7800 (t0)
REVERT: A  325 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.6643 (mp10)
REVERT: A  332 PHE cc_start: 0.8122 (m-10) cc_final: 0.7715 (m-10)
REVERT: B    8 TYR cc_start: 0.7522 (t80) cc_final: 0.7170 (t80)
REVERT: B   16 TRP cc_start: 0.8015 (m100) cc_final: 0.7726 (m100)
REVERT: B  213 TRP cc_start: 0.8595 (t60) cc_final: 0.7553 (t-100)
REVERT: B  283 ASN cc_start: 0.8427 (t0) cc_final: 0.8147 (t0)
REVERT: B  332 PHE cc_start: 0.8093 (m-10) cc_final: 0.7824 (m-10)
  outliers start: 19
  outliers final: 16
  residues processed: 135
  average time/residue: 0.2046
  time to fit residues: 35.4516
Evaluate side-chains
  138 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   chunk 61 optimal weight:    6.9990
   chunk 40 optimal weight:    0.3980
   chunk 45 optimal weight:   10.0000
   chunk 25 optimal weight:    0.2980
   chunk 8 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3849 r_free = 0.3849 target = 0.158291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.128471 restraints weight = 6876.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 2.31
r_work: 0.3217 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.1466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6378  Z= 0.168
  Angle     :  0.474   6.851   8692  Z= 0.241
  Chirality :  0.037   0.241   1072
  Planarity :  0.003   0.033   1058
  Dihedral  :  5.853  56.016   1096
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 17.42 %
    Favored  : 80.61 %
  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:  4.36 (0.29), residues: 786
  helix:  3.49 (0.18), residues: 686
  sheet:  None (None), residues: 0
  loop : -2.17 (0.56), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  16 
 HIS   0.002   0.001   HIS A 371 
 PHE   0.027   0.002   PHE A  62 
 TYR   0.015   0.001   TYR A   8 
 ARG   0.003   0.000   ARG A 295 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.635 
Fit side-chains
REVERT: A  164 ARG cc_start: 0.7053 (mtp85) cc_final: 0.6196 (mtp85)
REVERT: A  207 TYR cc_start: 0.8288 (t80) cc_final: 0.7821 (t80)
REVERT: A  213 TRP cc_start: 0.8566 (t60) cc_final: 0.7610 (t-100)
REVERT: A  245 MET cc_start: 0.6625 (mmp) cc_final: 0.6002 (mmp)
REVERT: A  283 ASN cc_start: 0.8099 (t0) cc_final: 0.7775 (t0)
REVERT: A  325 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.6566 (mp10)
REVERT: A  332 PHE cc_start: 0.8178 (m-10) cc_final: 0.7890 (m-10)
REVERT: B    8 TYR cc_start: 0.7452 (t80) cc_final: 0.7173 (t80)
REVERT: B   16 TRP cc_start: 0.7997 (m100) cc_final: 0.7694 (m100)
REVERT: B  213 TRP cc_start: 0.8578 (t60) cc_final: 0.7551 (t-100)
REVERT: B  283 ASN cc_start: 0.8428 (t0) cc_final: 0.8147 (t0)
REVERT: B  332 PHE cc_start: 0.8101 (m-10) cc_final: 0.7804 (m-10)
  outliers start: 13
  outliers final: 12
  residues processed: 128
  average time/residue: 0.2039
  time to fit residues: 33.8525
Evaluate side-chains
  132 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 75 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 45 optimal weight:    8.9990
   chunk 76 optimal weight:    0.6980
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3839 r_free = 0.3839 target = 0.157402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.127996 restraints weight = 6898.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 2.29
r_work: 0.3211 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6378  Z= 0.187
  Angle     :  0.483   7.268   8692  Z= 0.245
  Chirality :  0.038   0.239   1072
  Planarity :  0.003   0.032   1058
  Dihedral  :  5.638  54.001   1096
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.88 %
    Favored  : 79.39 %
  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:  4.37 (0.29), residues: 786
  helix:  3.46 (0.18), residues: 688
  sheet:  None (None), residues: 0
  loop : -2.01 (0.57), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  16 
 HIS   0.002   0.001   HIS A 371 
 PHE   0.029   0.002   PHE A  62 
 TYR   0.015   0.001   TYR A   8 
 ARG   0.003   0.000   ARG A 295 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 0.700 
Fit side-chains
REVERT: A    8 TYR cc_start: 0.7349 (t80) cc_final: 0.7129 (t80)
REVERT: A  164 ARG cc_start: 0.7002 (mtp85) cc_final: 0.6163 (mtp85)
REVERT: A  207 TYR cc_start: 0.8268 (t80) cc_final: 0.7766 (t80)
REVERT: A  213 TRP cc_start: 0.8581 (t60) cc_final: 0.7562 (t-100)
REVERT: A  283 ASN cc_start: 0.8060 (t0) cc_final: 0.7728 (t0)
REVERT: A  325 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.6439 (mp10)
REVERT: A  332 PHE cc_start: 0.8248 (m-10) cc_final: 0.7977 (m-10)
REVERT: B    8 TYR cc_start: 0.7544 (t80) cc_final: 0.7291 (t80)
REVERT: B   16 TRP cc_start: 0.7946 (m100) cc_final: 0.7607 (m100)
REVERT: B  213 TRP cc_start: 0.8593 (t60) cc_final: 0.7516 (t-100)
REVERT: B  283 ASN cc_start: 0.8393 (t0) cc_final: 0.8111 (t0)
REVERT: B  325 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.6827 (mp10)
REVERT: B  332 PHE cc_start: 0.8148 (m-10) cc_final: 0.7852 (m-10)
REVERT: B  342 GLU cc_start: 0.8494 (mp0) cc_final: 0.8153 (pm20)
  outliers start: 18
  outliers final: 15
  residues processed: 132
  average time/residue: 0.2070
  time to fit residues: 35.5703
Evaluate side-chains
  136 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  325 GLN
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 65 optimal weight:    0.3980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3830 r_free = 0.3830 target = 0.156551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.127205 restraints weight = 6917.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 2.27
r_work: 0.3220 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6378  Z= 0.203
  Angle     :  0.498   6.942   8692  Z= 0.251
  Chirality :  0.038   0.242   1072
  Planarity :  0.003   0.030   1058
  Dihedral  :  5.411  50.066   1096
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 18.79 %
    Favored  : 78.03 %
  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:  4.33 (0.29), residues: 786
  helix:  3.43 (0.18), residues: 688
  sheet:  None (None), residues: 0
  loop : -2.01 (0.57), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  16 
 HIS   0.002   0.001   HIS A 371 
 PHE   0.030   0.002   PHE B  62 
 TYR   0.014   0.001   TYR A   8 
 ARG   0.003   0.000   ARG A 295 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.690 
Fit side-chains
REVERT: A  164 ARG cc_start: 0.7076 (mtp85) cc_final: 0.6133 (mtp85)
REVERT: A  207 TYR cc_start: 0.8360 (t80) cc_final: 0.7857 (t80)
REVERT: A  213 TRP cc_start: 0.8603 (t60) cc_final: 0.7618 (t-100)
REVERT: A  283 ASN cc_start: 0.8156 (t0) cc_final: 0.7828 (t0)
REVERT: A  325 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.6506 (mp10)
REVERT: B   16 TRP cc_start: 0.7931 (m100) cc_final: 0.7576 (m100)
REVERT: B  213 TRP cc_start: 0.8613 (t60) cc_final: 0.7572 (t-100)
REVERT: B  283 ASN cc_start: 0.8476 (t0) cc_final: 0.8187 (t0)
REVERT: B  325 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.6869 (mp10)
REVERT: B  332 PHE cc_start: 0.8180 (m-10) cc_final: 0.7875 (m-10)
  outliers start: 21
  outliers final: 18
  residues processed: 133
  average time/residue: 0.1972
  time to fit residues: 33.9452
Evaluate side-chains
  138 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  325 GLN
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  378 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 64 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 48 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 73 optimal weight:    0.4980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.157077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.127981 restraints weight = 6925.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 2.26
r_work: 0.3220 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.1674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6378  Z= 0.189
  Angle     :  0.500   7.549   8692  Z= 0.252
  Chirality :  0.038   0.245   1072
  Planarity :  0.003   0.038   1058
  Dihedral  :  5.231  44.946   1096
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.79 %
    Favored  : 78.18 %
  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:  4.39 (0.29), residues: 786
  helix:  3.47 (0.18), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.97 (0.57), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  16 
 HIS   0.002   0.001   HIS A 371 
 PHE   0.030   0.002   PHE A  62 
 TYR   0.022   0.002   TYR B   8 
 ARG   0.004   0.000   ARG A 295 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.669 
Fit side-chains
REVERT: A    8 TYR cc_start: 0.7149 (t80) cc_final: 0.6904 (t80)
REVERT: A   26 ARG cc_start: 0.8055 (mtm110) cc_final: 0.7771 (mpp80)
REVERT: A  207 TYR cc_start: 0.8300 (t80) cc_final: 0.7785 (t80)
REVERT: A  213 TRP cc_start: 0.8569 (t60) cc_final: 0.7564 (t-100)
REVERT: A  283 ASN cc_start: 0.8091 (t0) cc_final: 0.7745 (t0)
REVERT: A  325 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.6424 (mp10)
REVERT: A  332 PHE cc_start: 0.8363 (m-80) cc_final: 0.8048 (m-10)
REVERT: B    8 TYR cc_start: 0.7159 (t80) cc_final: 0.6863 (t80)
REVERT: B   16 TRP cc_start: 0.7907 (m100) cc_final: 0.7531 (m100)
REVERT: B  213 TRP cc_start: 0.8602 (t60) cc_final: 0.7532 (t-100)
REVERT: B  283 ASN cc_start: 0.8453 (t0) cc_final: 0.8177 (t0)
REVERT: B  325 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.6807 (mp10)
REVERT: B  332 PHE cc_start: 0.8177 (m-10) cc_final: 0.7875 (m-10)
  outliers start: 20
  outliers final: 17
  residues processed: 134
  average time/residue: 0.1957
  time to fit residues: 33.9366
Evaluate side-chains
  140 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 121
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  325 GLN
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  378 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0270
   chunk 38 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.6440

-------------------------------------------------------------------------------
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 = 0.3836 r_free = 0.3836 target = 0.157310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.128110 restraints weight = 6972.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 2.28
r_work: 0.3221 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6378  Z= 0.188
  Angle     :  0.501   7.153   8692  Z= 0.252
  Chirality :  0.038   0.246   1072
  Planarity :  0.003   0.037   1058
  Dihedral  :  5.045  38.775   1096
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 18.64 %
    Favored  : 78.18 %
  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:  4.41 (0.29), residues: 786
  helix:  3.48 (0.18), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.95 (0.57), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  16 
 HIS   0.002   0.001   HIS A 371 
 PHE   0.030   0.002   PHE B  62 
 TYR   0.019   0.001   TYR B   8 
 ARG   0.008   0.001   ARG A 164 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.685 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.8065 (mtm110) cc_final: 0.7787 (mpp80)
REVERT: A  164 ARG cc_start: 0.6926 (mtp85) cc_final: 0.6710 (mtp85)
REVERT: A  207 TYR cc_start: 0.8297 (t80) cc_final: 0.7804 (t80)
REVERT: A  213 TRP cc_start: 0.8567 (t60) cc_final: 0.7569 (t-100)
REVERT: A  283 ASN cc_start: 0.8154 (t0) cc_final: 0.7826 (t0)
REVERT: A  325 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.6420 (mp10)
REVERT: A  332 PHE cc_start: 0.8393 (m-80) cc_final: 0.8154 (m-10)
REVERT: B    8 TYR cc_start: 0.6936 (t80) cc_final: 0.6700 (t80)
REVERT: B   16 TRP cc_start: 0.7904 (m100) cc_final: 0.7524 (m100)
REVERT: B   26 ARG cc_start: 0.7638 (mpp80) cc_final: 0.7302 (mpp80)
REVERT: B  213 TRP cc_start: 0.8603 (t60) cc_final: 0.7541 (t-100)
REVERT: B  283 ASN cc_start: 0.8463 (t0) cc_final: 0.8188 (t0)
REVERT: B  325 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.6812 (mp10)
REVERT: B  332 PHE cc_start: 0.8193 (m-10) cc_final: 0.7896 (m-10)
  outliers start: 21
  outliers final: 19
  residues processed: 135
  average time/residue: 0.1994
  time to fit residues: 34.8813
Evaluate side-chains
  138 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   55 CYS
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  300 CYS
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  325 GLN
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   55 CYS
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  311 THR
Chi-restraints excluded: chain B residue  325 GLN
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  378 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 41 optimal weight:    0.4980
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3829 r_free = 0.3829 target = 0.156681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.127262 restraints weight = 7088.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.31
r_work: 0.3197 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3047 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6378  Z= 0.208
  Angle     :  0.522   8.174   8692  Z= 0.260
  Chirality :  0.039   0.247   1072
  Planarity :  0.004   0.037   1058
  Dihedral  :  4.964  38.979   1096
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.94 %
    Favored  : 78.03 %
  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:  4.35 (0.29), residues: 786
  helix:  3.44 (0.18), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.95 (0.57), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  16 
 HIS   0.003   0.001   HIS A 371 
 PHE   0.030   0.002   PHE A  62 
 TYR   0.019   0.002   TYR B   8 
 ARG   0.007   0.001   ARG A 164 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3241.29 seconds
wall clock time: 58 minutes 14.69 seconds (3494.69 seconds total)