Starting phenix.real_space_refine
on Tue Mar 11 16:00:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p54_13194/03_2025/7p54_13194.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p54_13194/03_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_13194/03_2025/7p54_13194.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p54_13194/03_2025/7p54_13194.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p54_13194/03_2025/7p54_13194.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p54_13194/03_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-5624/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: 4.58, per 1000 atoms: 0.73
  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: 1.77
  Conformation dependent library (CDL) restraints added in 971.1 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: 0.52
  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: 1.81

  Time building geometry restraints manager: 2.09 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:             0.460
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.000
  Find NCS groups from input model:        0.540
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.240
-------------------------------------------------------------------------------
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  : 0.594 
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: 0.2009
  time to fit residues: 35.0633
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  : 0.688 
-------------------------------------------------------------------------------
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 = 0.120879 restraints weight = 6858.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.34
r_work: 0.3259 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3105 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
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  : 0.679 
Fit side-chains
REVERT: A  207 TYR cc_start: 0.8184 (t80) cc_final: 0.7776 (t80)
REVERT: A  213 TRP cc_start: 0.8561 (t60) cc_final: 0.7669 (t-100)
REVERT: A  332 PHE cc_start: 0.7906 (m-10) cc_final: 0.7689 (m-10)
REVERT: A  336 LEU cc_start: 0.8870 (mp) cc_final: 0.8649 (mp)
REVERT: B    8 TYR cc_start: 0.7729 (t80) cc_final: 0.7451 (t80)
REVERT: B   16 TRP cc_start: 0.8039 (m100) cc_final: 0.7822 (m100)
REVERT: B  213 TRP cc_start: 0.8557 (t60) cc_final: 0.7589 (t-100)
REVERT: B  283 ASN cc_start: 0.8218 (t0) cc_final: 0.7883 (t0)
REVERT: B  322 MET cc_start: 0.8412 (mtp) cc_final: 0.8053 (mtp)
  outliers start: 9
  outliers final: 6
  residues processed: 127
  average time/residue: 0.1938
  time to fit residues: 31.9534
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  : 0.614 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 64 optimal weight:    0.2980
   chunk 16 optimal weight:    0.5980
   chunk 65 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   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:    0.4980

-------------------------------------------------------------------------------
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 = 0.3865 r_free = 0.3865 target = 0.159586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.130313 restraints weight = 6864.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.28
r_work: 0.3260 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.1068

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= 0.166
  Angle     :  0.471   7.039   8692  Z= 0.240
  Chirality :  0.038   0.241   1072
  Planarity :  0.004   0.040   1058
  Dihedral  :  6.667  57.669   1096
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 11.36 %
    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:  4.31 (0.29), residues: 786
  helix:  3.57 (0.18), residues: 668
  sheet:  None (None), residues: 0
  loop : -2.05 (0.50), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  16 
 HIS   0.002   0.000   HIS A 371 
 PHE   0.022   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
  138 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 130
  time to evaluate  : 0.682 
Fit side-chains
REVERT: A  207 TYR cc_start: 0.8236 (t80) cc_final: 0.7807 (t80)
REVERT: A  213 TRP cc_start: 0.8527 (t60) cc_final: 0.7659 (t-100)
REVERT: A  245 MET cc_start: 0.6500 (mmp) cc_final: 0.5964 (mmp)
REVERT: A  283 ASN cc_start: 0.7958 (t0) cc_final: 0.7679 (t0)
REVERT: A  332 PHE cc_start: 0.8051 (m-10) cc_final: 0.7727 (m-10)
REVERT: A  336 LEU cc_start: 0.8899 (mp) cc_final: 0.8694 (mp)
REVERT: B    8 TYR cc_start: 0.7407 (t80) cc_final: 0.7050 (t80)
REVERT: B   16 TRP cc_start: 0.7981 (m100) cc_final: 0.7765 (m100)
REVERT: B  213 TRP cc_start: 0.8547 (t60) cc_final: 0.7600 (t-100)
REVERT: B  283 ASN cc_start: 0.8339 (t0) cc_final: 0.8001 (t0)
  outliers start: 8
  outliers final: 7
  residues processed: 133
  average time/residue: 0.1945
  time to fit residues: 34.0043
Evaluate side-chains
  132 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 125
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
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 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    0.0870
   chunk 28 optimal weight:    0.0370
   chunk 76 optimal weight:    1.9990
   chunk 56 optimal weight:    0.3980
   chunk 14 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   chunk 77 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 70 optimal weight:    0.2980
   overall best weight:    0.2836

-------------------------------------------------------------------------------
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 = 0.3870 r_free = 0.3870 target = 0.160439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.130495 restraints weight = 6917.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 2.33
r_work: 0.3342 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6378  Z= 0.135
  Angle     :  0.446   6.559   8692  Z= 0.230
  Chirality :  0.036   0.242   1072
  Planarity :  0.004   0.037   1058
  Dihedral  :  6.231  56.711   1096
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 14.39 %
    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:  4.47 (0.29), residues: 786
  helix:  3.63 (0.18), residues: 678
  sheet:  None (None), residues: 0
  loop : -2.24 (0.52), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  16 
 HIS   0.002   0.000   HIS A 371 
 PHE   0.025   0.002   PHE A  62 
 TYR   0.016   0.001   TYR A   8 
 ARG   0.003   0.000   ARG A  26 

*********************** 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
  143 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 0.683 
Fit side-chains
REVERT: A  207 TYR cc_start: 0.8231 (t80) cc_final: 0.7801 (t80)
REVERT: A  213 TRP cc_start: 0.8483 (t60) cc_final: 0.7681 (t-100)
REVERT: A  245 MET cc_start: 0.6465 (mmp) cc_final: 0.5887 (mmp)
REVERT: A  283 ASN cc_start: 0.8039 (t0) cc_final: 0.7751 (t0)
REVERT: A  332 PHE cc_start: 0.8050 (m-10) cc_final: 0.7709 (m-10)
REVERT: A  336 LEU cc_start: 0.8869 (mp) cc_final: 0.8653 (mp)
REVERT: B    8 TYR cc_start: 0.7348 (t80) cc_final: 0.7073 (t80)
REVERT: B   13 TRP cc_start: 0.8959 (p90) cc_final: 0.8483 (p90)
REVERT: B   16 TRP cc_start: 0.8006 (m100) cc_final: 0.7744 (m100)
REVERT: B  213 TRP cc_start: 0.8519 (t60) cc_final: 0.7619 (t-100)
REVERT: B  272 ASP cc_start: 0.8273 (m-30) cc_final: 0.8069 (m-30)
REVERT: B  283 ASN cc_start: 0.8418 (t0) cc_final: 0.8069 (t0)
  outliers start: 11
  outliers final: 11
  residues processed: 138
  average time/residue: 0.2001
  time to fit residues: 35.5916
Evaluate side-chains
  139 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 12 optimal weight:    0.2980
   chunk 46 optimal weight:    2.9990
   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 = 0.3853 r_free = 0.3853 target = 0.158556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.128599 restraints weight = 6980.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.33
r_work: 0.3277 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.1333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6378  Z= 0.186
  Angle     :  0.477   6.717   8692  Z= 0.241
  Chirality :  0.037   0.236   1072
  Planarity :  0.003   0.034   1058
  Dihedral  :  5.919  55.128   1096
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 15.76 %
    Favored  : 81.67 %
  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:  3.52 (0.18), residues: 686
  sheet:  None (None), residues: 0
  loop : -2.14 (0.56), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  13 
 HIS   0.002   0.001   HIS A 371 
 PHE   0.027   0.002   PHE B  62 
 TYR   0.015   0.001   TYR A   8 
 ARG   0.004   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
  141 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.640 
Fit side-chains
REVERT: A  207 TYR cc_start: 0.8295 (t80) cc_final: 0.7810 (t80)
REVERT: A  213 TRP cc_start: 0.8515 (t60) cc_final: 0.7659 (t-100)
REVERT: A  283 ASN cc_start: 0.8138 (t0) cc_final: 0.7833 (t0)
REVERT: A  325 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.6699 (mp10)
REVERT: A  332 PHE cc_start: 0.8087 (m-10) cc_final: 0.7680 (m-10)
REVERT: B    8 TYR cc_start: 0.7467 (t80) cc_final: 0.7163 (t80)
REVERT: B   16 TRP cc_start: 0.8002 (m100) cc_final: 0.7746 (m100)
REVERT: B  213 TRP cc_start: 0.8549 (t60) cc_final: 0.7609 (t-100)
REVERT: B  283 ASN cc_start: 0.8446 (t0) cc_final: 0.8168 (t0)
  outliers start: 17
  outliers final: 15
  residues processed: 133
  average time/residue: 0.1977
  time to fit residues: 33.9554
Evaluate side-chains
  139 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
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  254 LEU
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 A residue  334 VAL
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  268 VAL
Chi-restraints excluded: chain B residue  300 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 61 optimal weight:    8.9990
   chunk 40 optimal weight:    0.1980
   chunk 45 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0970
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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 = 0.3864 r_free = 0.3864 target = 0.159748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.130000 restraints weight = 6834.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 2.30
r_work: 0.3357 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6378  Z= 0.153
  Angle     :  0.468   6.998   8692  Z= 0.237
  Chirality :  0.037   0.241   1072
  Planarity :  0.003   0.034   1058
  Dihedral  :  5.670  52.976   1096
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 17.42 %
    Favored  : 80.15 %
  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:  4.48 (0.29), residues: 786
  helix:  3.57 (0.18), residues: 686
  sheet:  None (None), residues: 0
  loop : -2.15 (0.56), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  16 
 HIS   0.002   0.000   HIS A 371 
 PHE   0.028   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
  143 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 0.609 
Fit side-chains
REVERT: A    8 TYR cc_start: 0.7130 (t80) cc_final: 0.6728 (t80)
REVERT: A  207 TYR cc_start: 0.8278 (t80) cc_final: 0.7806 (t80)
REVERT: A  213 TRP cc_start: 0.8494 (t60) cc_final: 0.7654 (t-100)
REVERT: A  283 ASN cc_start: 0.8130 (t0) cc_final: 0.7816 (t0)
REVERT: A  325 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.6545 (mp10)
REVERT: A  332 PHE cc_start: 0.8203 (m-10) cc_final: 0.7926 (m-10)
REVERT: B    8 TYR cc_start: 0.7384 (t80) cc_final: 0.7120 (t80)
REVERT: B   16 TRP cc_start: 0.7977 (m100) cc_final: 0.7704 (m100)
REVERT: B  213 TRP cc_start: 0.8535 (t60) cc_final: 0.7619 (t-100)
REVERT: B  283 ASN cc_start: 0.8451 (t0) cc_final: 0.8174 (t0)
  outliers start: 16
  outliers final: 14
  residues processed: 136
  average time/residue: 0.1923
  time to fit residues: 33.7187
Evaluate side-chains
  142 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
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   27 LEU
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 75 optimal weight:    0.4980
   chunk 51 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0980
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 45 optimal weight:    8.9990
   chunk 76 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.158334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.128714 restraints weight = 6899.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 2.30
r_work: 0.3281 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.1523

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= 0.181
  Angle     :  0.486   7.069   8692  Z= 0.246
  Chirality :  0.037   0.239   1072
  Planarity :  0.003   0.033   1058
  Dihedral  :  5.449  49.158   1096
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  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:  4.46 (0.29), residues: 786
  helix:  3.53 (0.18), residues: 688
  sheet:  None (None), residues: 0
  loop : -2.03 (0.57), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  16 
 HIS   0.003   0.001   HIS A 371 
 PHE   0.028   0.002   PHE A  62 
 TYR   0.014   0.001   TYR A   8 
 ARG   0.008   0.001   ARG A 164 

*********************** 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
  143 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.622 
Fit side-chains
REVERT: A    8 TYR cc_start: 0.7212 (t80) cc_final: 0.6819 (t80)
REVERT: A  166 ASP cc_start: 0.8670 (p0) cc_final: 0.8464 (p0)
REVERT: A  207 TYR cc_start: 0.8319 (t80) cc_final: 0.7848 (t80)
REVERT: A  213 TRP cc_start: 0.8521 (t60) cc_final: 0.7649 (t-100)
REVERT: A  283 ASN cc_start: 0.8162 (t0) cc_final: 0.7850 (t0)
REVERT: A  325 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.6573 (mp10)
REVERT: A  332 PHE cc_start: 0.8264 (m-10) cc_final: 0.8014 (m-10)
REVERT: B    8 TYR cc_start: 0.7461 (t80) cc_final: 0.7198 (t80)
REVERT: B   16 TRP cc_start: 0.7989 (m100) cc_final: 0.7708 (m100)
REVERT: B  213 TRP cc_start: 0.8556 (t60) cc_final: 0.7616 (t-100)
REVERT: B  283 ASN cc_start: 0.8472 (t0) cc_final: 0.8200 (t0)
REVERT: B  325 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.6881 (mp10)
  outliers start: 18
  outliers final: 15
  residues processed: 136
  average time/residue: 0.1972
  time to fit residues: 34.6591
Evaluate side-chains
  140 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
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  254 LEU
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 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  268 VAL
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  325 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 41 optimal weight:    0.2980
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3833 r_free = 0.3833 target = 0.156850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.127565 restraints weight = 6911.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 2.28
r_work: 0.3206 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6378  Z= 0.210
  Angle     :  0.509   6.668   8692  Z= 0.257
  Chirality :  0.038   0.245   1072
  Planarity :  0.003   0.037   1058
  Dihedral  :  5.201  41.123   1096
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.09 %
    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:  4.37 (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   0.003   0.001   HIS A 371 
 PHE   0.031   0.002   PHE A  62 
 TYR   0.014   0.002   TYR A   8 
 ARG   0.003   0.001   ARG B 156 

*********************** 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
  139 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.598 
Fit side-chains
REVERT: A    8 TYR cc_start: 0.7362 (t80) cc_final: 0.7161 (t80)
REVERT: A  164 ARG cc_start: 0.7146 (mtp85) cc_final: 0.6346 (mtp85)
REVERT: A  207 TYR cc_start: 0.8360 (t80) cc_final: 0.7839 (t80)
REVERT: A  213 TRP cc_start: 0.8574 (t60) cc_final: 0.7607 (t-100)
REVERT: A  283 ASN cc_start: 0.8177 (t0) cc_final: 0.7878 (t0)
REVERT: A  325 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.6506 (mp10)
REVERT: B    8 TYR cc_start: 0.7630 (t80) cc_final: 0.7391 (t80)
REVERT: B   16 TRP cc_start: 0.7935 (m100) cc_final: 0.7580 (m100)
REVERT: B  213 TRP cc_start: 0.8604 (t60) cc_final: 0.7568 (t-100)
REVERT: B  283 ASN cc_start: 0.8453 (t0) cc_final: 0.8181 (t0)
REVERT: B  325 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.6857 (mp10)
  outliers start: 19
  outliers final: 16
  residues processed: 132
  average time/residue: 0.1888
  time to fit residues: 32.2989
Evaluate side-chains
  137 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  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  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  334 VAL
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  268 VAL
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  325 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 66 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0570
   overall best weight:    0.5498

-------------------------------------------------------------------------------
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 = 0.3844 r_free = 0.3844 target = 0.158048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.129000 restraints weight = 6884.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.28
r_work: 0.3237 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.1650

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= 0.166
  Angle     :  0.487   6.989   8692  Z= 0.246
  Chirality :  0.038   0.248   1072
  Planarity :  0.003   0.037   1058
  Dihedral  :  5.019  38.749   1096
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 19.85 %
    Favored  : 77.58 %
  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:  4.49 (0.29), residues: 786
  helix:  3.54 (0.18), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.96 (0.57), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  16 
 HIS   0.003   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 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
  137 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.670 
Fit side-chains
REVERT: A  207 TYR cc_start: 0.8311 (t80) cc_final: 0.7814 (t80)
REVERT: A  213 TRP cc_start: 0.8543 (t60) cc_final: 0.7614 (t-100)
REVERT: A  283 ASN cc_start: 0.8149 (t0) cc_final: 0.7819 (t0)
REVERT: A  325 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.6461 (mp10)
REVERT: A  332 PHE cc_start: 0.8382 (m-80) cc_final: 0.8078 (m-10)
REVERT: B   16 TRP cc_start: 0.7912 (m100) cc_final: 0.7562 (m100)
REVERT: B  213 TRP cc_start: 0.8579 (t60) cc_final: 0.7577 (t-100)
REVERT: B  283 ASN cc_start: 0.8444 (t0) cc_final: 0.8167 (t0)
REVERT: B  325 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.6984 (mp10)
  outliers start: 17
  outliers final: 15
  residues processed: 131
  average time/residue: 0.1922
  time to fit residues: 32.7928
Evaluate side-chains
  137 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
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  334 VAL
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  268 VAL
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  325 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   chunk 69 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   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 = 0.3840 r_free = 0.3840 target = 0.157660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.128320 restraints weight = 6976.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 2.30
r_work: 0.3221 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.1727

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= 0.189
  Angle     :  0.503   7.341   8692  Z= 0.253
  Chirality :  0.038   0.245   1072
  Planarity :  0.003   0.036   1058
  Dihedral  :  4.924  38.724   1096
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 19.70 %
    Favored  : 77.73 %
  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:  4.43 (0.29), residues: 786
  helix:  3.50 (0.18), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.96 (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   0.017   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
  137 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.769 
Fit side-chains
REVERT: A  164 ARG cc_start: 0.6962 (mtp85) cc_final: 0.6759 (mtp85)
REVERT: A  176 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7277 (tt0)
REVERT: A  207 TYR cc_start: 0.8324 (t80) cc_final: 0.7845 (t80)
REVERT: A  213 TRP cc_start: 0.8555 (t60) cc_final: 0.7548 (t-100)
REVERT: A  283 ASN cc_start: 0.8194 (t0) cc_final: 0.7882 (t0)
REVERT: A  325 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.6461 (mp10)
REVERT: A  332 PHE cc_start: 0.8415 (m-80) cc_final: 0.8190 (m-10)
REVERT: B    8 TYR cc_start: 0.7293 (t80) cc_final: 0.6946 (t80)
REVERT: B   16 TRP cc_start: 0.7911 (m100) cc_final: 0.7560 (m100)
REVERT: B  213 TRP cc_start: 0.8592 (t60) cc_final: 0.7517 (t-100)
REVERT: B  283 ASN cc_start: 0.8445 (t0) cc_final: 0.8165 (t0)
REVERT: B  325 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.6845 (mp10)
REVERT: B  332 PHE cc_start: 0.8230 (m-10) cc_final: 0.7951 (m-10)
  outliers start: 17
  outliers final: 15
  residues processed: 131
  average time/residue: 0.2025
  time to fit residues: 34.2840
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  : 0.704 
-------------------------------------------------------------------------------
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  268 VAL
Chi-restraints excluded: chain B residue  300 CYS
Chi-restraints excluded: chain B residue  325 GLN
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:    0.5980
   chunk 70 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 41 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3880 r_free = 0.3880 target = 0.160811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.132431 restraints weight = 6983.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 2.25
r_work: 0.3238 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6378  Z= 0.202
  Angle     :  0.508   7.062   8692  Z= 0.255
  Chirality :  0.039   0.247   1072
  Planarity :  0.003   0.036   1058
  Dihedral  :  4.939  38.932   1096
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.39 %
    Favored  : 77.73 %
  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 : -1.96 (0.56), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  16 
 HIS   0.003   0.001   HIS A 371 
 PHE   0.030   0.002   PHE A  62 
 TYR   0.020   0.001   TYR B 216 
 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: 3299.96 seconds
wall clock time: 57 minutes 31.03 seconds (3451.03 seconds total)