Starting phenix.real_space_refine
on Tue Feb 11 16:28:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p5j_13200/02_2025/7p5j_13200.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p5j_13200/02_2025/7p5j_13200.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p5j_13200/02_2025/7p5j_13200.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p5j_13200/02_2025/7p5j_13200.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p5j_13200/02_2025/7p5j_13200.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p5j_13200/02_2025/7p5j_13200.cif"
  }
  resolution = 4.0
  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      24      5.16       5
     C    4034      2.51       5
     N    1036      2.21       5
     O    1156      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6250
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3069
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3069
          Classifications: {'peptide': 399}
          Link IDs: {'PTRANS': 17, 'TRANS': 381}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3069
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 3069
          Classifications: {'peptide': 399}
          Link IDs: {'PTRANS': 17, 'TRANS': 381}
          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: "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: 4.21, per 1000 atoms: 0.67
  Number of scatterers: 6250
  At special positions: 0
  Unit cell: (88.536, 71.61, 134.106, 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      24     16.00
     O    1156      8.00
     N    1036      7.00
     C    4034      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 275 " - pdb=" SG  CYS A 385 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 303 " - pdb=" SG  CYS A 370 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 275 " - pdb=" SG  CYS B 385 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 303 " - pdb=" SG  CYS B 370 " 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-ASN
      " NAG A 501 " - " ASN A 284 "
      " NAG A 502 " - " ASN A 355 "
      " NAG B 501 " - " ASN B 284 "
      " NAG B 502 " - " ASN B 355 "
      " NAG C   1 " - " ASN A 130 "
      " NAG D   1 " - " ASN B 130 "
  Time building additional restraints: 1.66
  Conformation dependent library (CDL) restraints added in 918.3 milliseconds
  

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1496

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 0 sheets defined
      86.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 18
      removed outlier: 3.604A  pdb=" N   HIS A  14 " --> pdb=" O   SER A  10 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 70
      removed outlier: 3.591A  pdb=" N   GLN A  41 " --> pdb=" O   GLU A  37 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   VAL A  47 " --> pdb=" O   ALA A  43 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ALA A  48 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 161
    Processing helix  chain 'A' and resid 167 through 187
    Processing helix  chain 'A' and resid 198 through 238
      removed outlier: 3.636A  pdb=" N   VAL A 202 " --> pdb=" O   SER A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 276
      removed outlier: 4.116A  pdb=" N   VAL A 248 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   MET A 249 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 290
    Processing helix  chain 'A' and resid 293 through 303
      removed outlier: 3.755A  pdb=" N   LEU A 297 " --> pdb=" O   SER A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 335
      removed outlier: 3.759A  pdb=" N   ARG A 320 " --> pdb=" O   THR A 316 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   GLN A 328 " --> pdb=" O   ASN A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 340
      removed outlier: 3.805A  pdb=" N   GLN A 339 " --> pdb=" O   GLU A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 368
      removed outlier: 3.565A  pdb=" N   LYS A 345 " --> pdb=" O   PRO A 341 " (cutoff:3.500A)
      Proline residue:  A 346  - end of helix
      removed outlier: 4.183A  pdb=" N   SER A 349 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 386
      removed outlier: 4.266A  pdb=" N   LEU A 373 " --> pdb=" O   HIS A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 418
      Proline residue:  A 414  - end of helix
      removed outlier: 4.580A  pdb=" N   ALA A 418 " --> pdb=" O   PRO A 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 18
    Processing helix  chain 'B' and resid 37 through 70
      removed outlier: 3.620A  pdb=" N   ALA B  48 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 161
    Processing helix  chain 'B' and resid 167 through 190
      removed outlier: 3.694A  pdb=" N   ALA B 190 " --> pdb=" O   LEU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 238
      removed outlier: 3.757A  pdb=" N   VAL B 202 " --> pdb=" O   SER B 198 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ASN B 205 " --> pdb=" O   GLN B 201 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   VAL B 206 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 239 through 275
      removed outlier: 4.010A  pdb=" N   VAL B 248 " --> pdb=" O   ILE B 244 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   MET B 249 " --> pdb=" O   VAL B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 290
    Processing helix  chain 'B' and resid 293 through 303
    Processing helix  chain 'B' and resid 311 through 335
    Processing helix  chain 'B' and resid 335 through 340
      removed outlier: 3.925A  pdb=" N   GLN B 339 " --> pdb=" O   GLU B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 343 through 368
    Processing helix  chain 'B' and resid 369 through 385
      removed outlier: 4.120A  pdb=" N   LEU B 373 " --> pdb=" O   HIS B 369 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LYS B 375 " --> pdb=" O   ARG B 371 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   ASP B 376 " --> pdb=" O   SER B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 418
      Proline residue:  B 414  - end of helix
      removed outlier: 4.576A  pdb=" N   ALA B 418 " --> pdb=" O   PRO B 414 " (cutoff:3.500A)

    552 hydrogen bonds defined for protein.
    1656 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: 1.80

  Time building geometry restraints manager: 1.91 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: 1975
        1.34 -     1.46: 1103
        1.46 -     1.58: 3270
        1.58 -     1.70: 0
        1.70 -     1.82: 30
  Bond restraints: 6378
  Sorted by residual:
  bond pdb=" N   ILE B 244 "
       pdb=" CA  ILE B 244 "
    ideal  model  delta    sigma   weight residual
    1.461  1.499 -0.038 1.19e-02 7.06e+03 1.03e+01
  bond pdb=" CA  PRO A 421 "
       pdb=" C   PRO A 421 "
    ideal  model  delta    sigma   weight residual
    1.517  1.545 -0.028 9.30e-03 1.16e+04 9.10e+00
  bond pdb=" N   VAL B 243 "
       pdb=" CA  VAL B 243 "
    ideal  model  delta    sigma   weight residual
    1.463  1.495 -0.032 1.14e-02 7.69e+03 8.03e+00
  bond pdb=" N   ASP B 137 "
       pdb=" CA  ASP B 137 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.79e+00
  bond pdb=" N   LEU B 242 "
       pdb=" CA  LEU B 242 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.16e-02 7.43e+03 6.65e+00
  ... (remaining 6373 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 8296
        1.50 -     3.00: 297
        3.00 -     4.50: 77
        4.50 -     6.00: 29
        6.00 -     7.51: 5
  Bond angle restraints: 8704
  Sorted by residual:
  angle pdb=" N   PRO A 421 "
        pdb=" CA  PRO A 421 "
        pdb=" C   PRO A 421 "
      ideal   model   delta    sigma   weight residual
     110.70  116.89   -6.19 1.22e+00 6.72e-01 2.57e+01
  angle pdb=" CA  PRO B 421 "
        pdb=" C   PRO B 421 "
        pdb=" N   PRO B 422 "
      ideal   model   delta    sigma   weight residual
     117.93  123.81   -5.88 1.20e+00 6.94e-01 2.40e+01
  angle pdb=" CA  PRO A 421 "
        pdb=" C   PRO A 421 "
        pdb=" N   PRO A 422 "
      ideal   model   delta    sigma   weight residual
     117.93  123.57   -5.64 1.20e+00 6.94e-01 2.21e+01
  angle pdb=" O   PRO B 421 "
        pdb=" C   PRO B 421 "
        pdb=" N   PRO B 422 "
      ideal   model   delta    sigma   weight residual
     121.46  116.44    5.02 1.18e+00 7.18e-01 1.81e+01
  angle pdb=" CA  ASP B 137 "
        pdb=" CB  ASP B 137 "
        pdb=" CG  ASP B 137 "
      ideal   model   delta    sigma   weight residual
     112.60  116.68   -4.08 1.00e+00 1.00e+00 1.67e+01
  ... (remaining 8699 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.06: 3516
       21.06 -    42.12: 296
       42.12 -    63.18: 58
       63.18 -    84.24: 15
       84.24 -   105.30: 15
  Dihedral angle restraints: 3900
    sinusoidal: 1590
      harmonic: 2310
  Sorted by residual:
  dihedral pdb=" CB  CYS B 303 "
           pdb=" SG  CYS B 303 "
           pdb=" SG  CYS B 370 "
           pdb=" CB  CYS B 370 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    9.23   83.77     1      1.00e+01 1.00e-02 8.56e+01
  dihedral pdb=" CA  ASP B 279 "
           pdb=" C   ASP B 279 "
           pdb=" N   PRO B 280 "
           pdb=" CA  PRO B 280 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.22   18.78     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" C2  NAG C   2 "
           pdb=" C3  NAG C   2 "
           pdb=" C4  NAG C   2 "
           pdb=" O4  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   69.81  105.30     1      3.00e+01 1.11e-03 1.35e+01
  ... (remaining 3897 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 930
       0.061 -    0.122: 131
       0.122 -    0.182: 8
       0.182 -    0.243: 2
       0.243 -    0.304: 1
  Chirality restraints: 1072
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-02 2.50e+03 1.39e+02
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 130 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.10   -0.30 2.00e-01 2.50e+01 2.31e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN B 130 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.16   -0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 1069 not shown)

  Planarity restraints: 1092
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "    0.295 2.00e-02 2.50e+03   2.56e-01 8.19e+02
        pdb=" C7  NAG D   2 "   -0.067 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "    0.158 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "   -0.454 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "    0.068 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "   -0.266 2.00e-02 2.50e+03   2.21e-01 6.13e+02
        pdb=" C7  NAG D   1 "    0.073 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "   -0.183 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "    0.368 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 130 "   -0.025 2.00e-02 2.50e+03   2.36e-02 6.95e+00
        pdb=" CG  ASN A 130 "    0.036 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 130 "   -0.007 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 130 "    0.018 2.00e-02 2.50e+03
        pdb=" C1  NAG C   1 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1089 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1361
        2.79 -     3.32: 6914
        3.32 -     3.85: 10669
        3.85 -     4.37: 11531
        4.37 -     4.90: 19376
  Nonbonded interactions: 49851
  Sorted by model distance:
  nonbonded pdb=" O   GLU B 154 "
            pdb=" OG1 THR B 157 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   GLU A 154 "
            pdb=" OG1 THR A 157 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   VAL A  90 "
            pdb=" OG  SER A  93 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O3  NAG C   1 "
            pdb=" O7  NAG C   2 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" OD1 ASN A 205 "
            pdb=" N   VAL A 206 "
     model   vdw
     2.344 3.120
  ... (remaining 49846 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.760
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.810
  Find NCS groups from input model:        0.220
  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:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
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   0.051   6378  Z= 0.262
  Angle     :  0.725   7.505   8704  Z= 0.405
  Chirality :  0.043   0.304   1072
  Planarity :  0.011   0.256   1086
  Dihedral  : 17.475 105.301   2392
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  1.51 %
    Favored  : 97.89 %
  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:  2.65 (0.31), residues: 790
  helix:  2.36 (0.20), residues: 658
  sheet:  None (None), residues: 0
  loop : -1.51 (0.54), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 258 
 HIS   0.004   0.001   HIS B 128 
 PHE   0.029   0.002   PHE B 208 
 TYR   0.026   0.002   TYR A 299 
 ARG   0.004   0.000   ARG A 314 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 239
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
REVERT: A  273 ASP cc_start: 0.7622 (t70) cc_final: 0.6956 (t70)
REVERT: A  350 LEU cc_start: 0.8933 (mt) cc_final: 0.8660 (mt)
REVERT: B   40 TYR cc_start: 0.7595 (t80) cc_final: 0.7385 (t80)
REVERT: B   98 LEU cc_start: 0.8265 (mm) cc_final: 0.8063 (mm)
REVERT: B  134 SER cc_start: 0.8916 (m) cc_final: 0.8442 (t)
REVERT: B  160 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8679 (tm-30)
REVERT: B  167 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7288 (tp30)
REVERT: B  304 ASN cc_start: 0.8119 (m-40) cc_final: 0.7634 (m-40)
  outliers start: 4
  outliers final: 2
  residues processed: 241
  average time/residue: 0.1429
  time to fit residues: 47.2440
Evaluate side-chains
  204 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 202
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  240 LYS
Chi-restraints excluded: chain B residue  244 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:   10.0000
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
B 128 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.153477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.132389 restraints weight = 9925.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.135677 restraints weight = 5996.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.137824 restraints weight = 4168.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6378  Z= 0.269
  Angle     :  0.736   9.467   8704  Z= 0.345
  Chirality :  0.045   0.216   1072
  Planarity :  0.005   0.069   1086
  Dihedral  : 10.271  73.400   1024
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.01 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.00 (0.30), residues: 790
  helix:  2.55 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.31 (0.57), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 258 
 HIS   0.006   0.001   HIS B  17 
 PHE   0.034   0.002   PHE A 208 
 TYR   0.021   0.002   TYR A 377 
 ARG   0.003   0.000   ARG B 173 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 219
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A   40 TYR cc_start: 0.7956 (t80) cc_final: 0.7745 (t80)
REVERT: A  131 HIS cc_start: 0.8144 (t70) cc_final: 0.7891 (t70)
REVERT: A  273 ASP cc_start: 0.7523 (t70) cc_final: 0.7161 (t70)
REVERT: A  381 LEU cc_start: 0.8651 (mt) cc_final: 0.8427 (mt)
REVERT: B  134 SER cc_start: 0.9013 (m) cc_final: 0.8155 (t)
REVERT: B  304 ASN cc_start: 0.8254 (m-40) cc_final: 0.7736 (m-40)
  outliers start: 16
  outliers final: 11
  residues processed: 224
  average time/residue: 0.1481
  time to fit residues: 45.2384
Evaluate side-chains
  216 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 205
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  279 ASP
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  347 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0470
   chunk 22 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.7078

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

Flipped N/Q/H residues before XYZ refinement:
B 128 HIS
B 324 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.156114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.134847 restraints weight = 10045.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.138434 restraints weight = 6013.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.140731 restraints weight = 4141.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6378  Z= 0.205
  Angle     :  0.691  10.209   8704  Z= 0.322
  Chirality :  0.041   0.182   1072
  Planarity :  0.005   0.064   1086
  Dihedral  :  8.041  57.456   1018
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 17.98 %
    Favored  : 79.46 %
  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:  3.17 (0.30), residues: 790
  helix:  2.68 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.35 (0.58), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 258 
 HIS   0.005   0.001   HIS B 326 
 PHE   0.035   0.002   PHE B 208 
 TYR   0.025   0.002   TYR A 299 
 ARG   0.002   0.000   ARG A  21 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 212
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.7921 (t80) cc_final: 0.7669 (t80)
REVERT: A  273 ASP cc_start: 0.7658 (t70) cc_final: 0.7182 (t70)
REVERT: A  381 LEU cc_start: 0.8710 (mt) cc_final: 0.8336 (mt)
REVERT: A  402 SER cc_start: 0.8751 (p) cc_final: 0.8216 (t)
REVERT: B  134 SER cc_start: 0.8992 (m) cc_final: 0.8177 (t)
REVERT: B  214 TRP cc_start: 0.6931 (t60) cc_final: 0.6475 (t60)
REVERT: B  240 LYS cc_start: 0.7597 (mttp) cc_final: 0.7285 (mttp)
REVERT: B  304 ASN cc_start: 0.8197 (m-40) cc_final: 0.7772 (m-40)
REVERT: B  381 LEU cc_start: 0.8602 (mt) cc_final: 0.8224 (mt)
REVERT: B  402 SER cc_start: 0.8685 (p) cc_final: 0.8178 (t)
  outliers start: 17
  outliers final: 14
  residues processed: 220
  average time/residue: 0.1455
  time to fit residues: 44.5455
Evaluate side-chains
  215 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 201
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  350 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 77 optimal weight:    5.9990
   chunk 63 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 70 optimal weight:    0.5980
   chunk 71 optimal weight:    0.0060
   chunk 68 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
B 128 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.157510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.136046 restraints weight = 10226.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.139667 restraints weight = 6059.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.141996 restraints weight = 4144.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6378  Z= 0.199
  Angle     :  0.690  11.129   8704  Z= 0.318
  Chirality :  0.040   0.208   1072
  Planarity :  0.005   0.059   1086
  Dihedral  :  7.022  55.873   1018
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 19.34 %
    Favored  : 77.19 %
  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:  3.20 (0.30), residues: 790
  helix:  2.73 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.55 (0.56), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 258 
 HIS   0.005   0.001   HIS B 326 
 PHE   0.028   0.002   PHE B 208 
 TYR   0.025   0.002   TYR A 299 
 ARG   0.002   0.000   ARG A 314 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 215
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.7975 (t80) cc_final: 0.7698 (t80)
REVERT: A  273 ASP cc_start: 0.7643 (t70) cc_final: 0.7111 (t70)
REVERT: A  381 LEU cc_start: 0.8635 (mt) cc_final: 0.8270 (mt)
REVERT: A  402 SER cc_start: 0.8699 (p) cc_final: 0.8180 (t)
REVERT: B  134 SER cc_start: 0.9008 (m) cc_final: 0.8142 (t)
REVERT: B  214 TRP cc_start: 0.6716 (t60) cc_final: 0.6452 (t60)
REVERT: B  240 LYS cc_start: 0.7561 (mttp) cc_final: 0.7273 (mttp)
REVERT: B  246 MET cc_start: 0.7670 (ppp) cc_final: 0.6532 (ppp)
REVERT: B  304 ASN cc_start: 0.8274 (m-40) cc_final: 0.7920 (m-40)
REVERT: B  381 LEU cc_start: 0.8583 (mt) cc_final: 0.8031 (mt)
REVERT: B  402 SER cc_start: 0.8669 (p) cc_final: 0.8231 (t)
  outliers start: 23
  outliers final: 17
  residues processed: 223
  average time/residue: 0.1448
  time to fit residues: 44.3501
Evaluate side-chains
  216 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 199
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  142 GLU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  392 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 6 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A  17 HIS
B 138 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.154280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.135914 restraints weight = 10218.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.140244 restraints weight = 6010.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.140744 restraints weight = 3775.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   6378  Z= 0.230
  Angle     :  0.724  13.992   8704  Z= 0.328
  Chirality :  0.041   0.162   1072
  Planarity :  0.005   0.056   1086
  Dihedral  :  6.736  59.893   1018
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 21.60 %
    Favored  : 74.92 %
  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:  3.17 (0.30), residues: 790
  helix:  2.73 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.66 (0.54), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 258 
 HIS   0.009   0.001   HIS B 138 
 PHE   0.017   0.002   PHE B 208 
 TYR   0.017   0.002   TYR A 299 
 ARG   0.002   0.000   ARG B 213 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 210
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8118 (t80) cc_final: 0.7882 (t80)
REVERT: A   61 PHE cc_start: 0.7430 (m-80) cc_final: 0.7159 (m-80)
REVERT: A  273 ASP cc_start: 0.7704 (t70) cc_final: 0.7154 (t70)
REVERT: A  353 THR cc_start: 0.8813 (t) cc_final: 0.8605 (t)
REVERT: A  381 LEU cc_start: 0.8557 (mt) cc_final: 0.8043 (mt)
REVERT: A  402 SER cc_start: 0.8535 (p) cc_final: 0.8010 (t)
REVERT: B  134 SER cc_start: 0.9083 (m) cc_final: 0.8116 (t)
REVERT: B  240 LYS cc_start: 0.7553 (mttp) cc_final: 0.7278 (mttp)
REVERT: B  246 MET cc_start: 0.7506 (ppp) cc_final: 0.6214 (ppp)
REVERT: B  304 ASN cc_start: 0.8288 (m-40) cc_final: 0.7845 (m-40)
REVERT: B  381 LEU cc_start: 0.8709 (mt) cc_final: 0.8042 (mt)
REVERT: B  402 SER cc_start: 0.8630 (p) cc_final: 0.8105 (t)
  outliers start: 23
  outliers final: 20
  residues processed: 221
  average time/residue: 0.1497
  time to fit residues: 45.0761
Evaluate side-chains
  225 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 205
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  138 HIS
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  392 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 57 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
B 138 HIS
B 324 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.154243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.134545 restraints weight = 10127.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.137557 restraints weight = 6299.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.139683 restraints weight = 4479.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6378  Z= 0.227
  Angle     :  0.742  15.322   8704  Z= 0.336
  Chirality :  0.041   0.215   1072
  Planarity :  0.005   0.052   1086
  Dihedral  :  6.670  58.829   1018
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 22.96 %
    Favored  : 72.81 %
  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:  3.12 (0.30), residues: 790
  helix:  2.68 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.63 (0.54), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 258 
 HIS   0.016   0.001   HIS B 138 
 PHE   0.017   0.002   PHE B 208 
 TYR   0.017   0.002   TYR A 299 
 ARG   0.004   0.000   ARG A 177 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 203
  time to evaluate  : 0.644 
Fit side-chains
REVERT: A   40 TYR cc_start: 0.8113 (t80) cc_final: 0.7861 (t80)
REVERT: A   61 PHE cc_start: 0.7397 (m-80) cc_final: 0.7120 (m-80)
REVERT: A  273 ASP cc_start: 0.7754 (t70) cc_final: 0.7210 (t70)
REVERT: A  381 LEU cc_start: 0.8579 (mt) cc_final: 0.8000 (mt)
REVERT: A  402 SER cc_start: 0.8639 (p) cc_final: 0.8110 (t)
REVERT: B  134 SER cc_start: 0.9080 (m) cc_final: 0.8041 (t)
REVERT: B  240 LYS cc_start: 0.7503 (mttp) cc_final: 0.7214 (mttp)
REVERT: B  304 ASN cc_start: 0.8242 (m-40) cc_final: 0.7884 (t0)
REVERT: B  381 LEU cc_start: 0.8701 (mt) cc_final: 0.8032 (mt)
REVERT: B  402 SER cc_start: 0.8677 (p) cc_final: 0.8167 (t)
  outliers start: 28
  outliers final: 23
  residues processed: 216
  average time/residue: 0.1507
  time to fit residues: 45.1521
Evaluate side-chains
  221 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 198
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  138 HIS
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  358 GLU
Chi-restraints excluded: chain B residue  392 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 75 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0040
   chunk 77 optimal weight:    0.9980
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
B 138 HIS
B 324 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.155117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.136783 restraints weight = 10026.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.140976 restraints weight = 5901.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.141743 restraints weight = 3820.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   6378  Z= 0.215
  Angle     :  0.760  15.437   8704  Z= 0.345
  Chirality :  0.042   0.318   1072
  Planarity :  0.005   0.048   1086
  Dihedral  :  6.566  58.333   1018
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 23.72 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.14 (0.30), residues: 790
  helix:  2.68 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.53 (0.54), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 258 
 HIS   0.012   0.001   HIS B 138 
 PHE   0.016   0.001   PHE B 208 
 TYR   0.018   0.002   TYR A 299 
 ARG   0.003   0.000   ARG A 177 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 205
  time to evaluate  : 0.705 
Fit side-chains
REVERT: A   40 TYR cc_start: 0.8136 (t80) cc_final: 0.7860 (t80)
REVERT: A   61 PHE cc_start: 0.7310 (m-80) cc_final: 0.7051 (m-80)
REVERT: A   95 ILE cc_start: 0.8377 (mp) cc_final: 0.8168 (mm)
REVERT: A  273 ASP cc_start: 0.7638 (t70) cc_final: 0.7180 (t70)
REVERT: A  330 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8603 (mt)
REVERT: A  381 LEU cc_start: 0.8624 (mt) cc_final: 0.8035 (mt)
REVERT: A  402 SER cc_start: 0.8605 (p) cc_final: 0.8081 (t)
REVERT: B  134 SER cc_start: 0.8876 (m) cc_final: 0.7832 (t)
REVERT: B  240 LYS cc_start: 0.7466 (mttp) cc_final: 0.7166 (mttp)
REVERT: B  246 MET cc_start: 0.7069 (ppp) cc_final: 0.5706 (ppp)
REVERT: B  304 ASN cc_start: 0.8156 (m-40) cc_final: 0.7886 (t0)
REVERT: B  381 LEU cc_start: 0.8709 (mt) cc_final: 0.8057 (mt)
REVERT: B  402 SER cc_start: 0.8671 (p) cc_final: 0.8098 (t)
  outliers start: 25
  outliers final: 22
  residues processed: 218
  average time/residue: 0.1464
  time to fit residues: 43.9132
Evaluate side-chains
  222 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 199
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  138 HIS
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  358 GLU
Chi-restraints excluded: chain B residue  392 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 32 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
A 360 ASN
B 138 HIS
B 324 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.155616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.136533 restraints weight = 9994.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.138184 restraints weight = 6955.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.139357 restraints weight = 5553.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   6378  Z= 0.230
  Angle     :  0.764  15.855   8704  Z= 0.346
  Chirality :  0.042   0.297   1072
  Planarity :  0.005   0.050   1086
  Dihedral  :  6.503  57.347   1018
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 24.32 %
    Favored  : 71.60 %
  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:  3.18 (0.30), residues: 790
  helix:  2.68 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -1.36 (0.55), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 258 
 HIS   0.014   0.001   HIS B 138 
 PHE   0.017   0.001   PHE B 208 
 TYR   0.020   0.002   TYR A 299 
 ARG   0.006   0.000   ARG B 382 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 205
  time to evaluate  : 0.613 
Fit side-chains
REVERT: A   40 TYR cc_start: 0.8244 (t80) cc_final: 0.7946 (t80)
REVERT: A   61 PHE cc_start: 0.7135 (m-80) cc_final: 0.6882 (m-80)
REVERT: A  273 ASP cc_start: 0.7714 (t70) cc_final: 0.7160 (t70)
REVERT: A  330 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8557 (mt)
REVERT: A  381 LEU cc_start: 0.8601 (mt) cc_final: 0.7987 (mt)
REVERT: A  402 SER cc_start: 0.8579 (p) cc_final: 0.8080 (t)
REVERT: B  134 SER cc_start: 0.8872 (m) cc_final: 0.7842 (t)
REVERT: B  240 LYS cc_start: 0.7486 (mttp) cc_final: 0.7219 (mttp)
REVERT: B  246 MET cc_start: 0.7417 (ppp) cc_final: 0.5998 (ppp)
REVERT: B  304 ASN cc_start: 0.8245 (m-40) cc_final: 0.7872 (t0)
REVERT: B  381 LEU cc_start: 0.8706 (mt) cc_final: 0.8032 (mt)
REVERT: B  402 SER cc_start: 0.8715 (p) cc_final: 0.8109 (t)
  outliers start: 27
  outliers final: 22
  residues processed: 219
  average time/residue: 0.1459
  time to fit residues: 43.9149
Evaluate side-chains
  219 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 196
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  358 GLU
Chi-restraints excluded: chain B residue  392 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 64 optimal weight:    0.6980
   chunk 1 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 41 optimal weight:    0.4980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 324 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.155425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.136791 restraints weight = 10012.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.138345 restraints weight = 6840.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.139731 restraints weight = 5554.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.086   6378  Z= 0.224
  Angle     :  0.769  16.080   8704  Z= 0.350
  Chirality :  0.042   0.261   1072
  Planarity :  0.005   0.054   1086
  Dihedral  :  6.456  57.027   1018
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 25.53 %
    Favored  : 71.00 %
  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:  3.17 (0.30), residues: 790
  helix:  2.66 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.19 (0.57), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 258 
 HIS   0.005   0.001   HIS B 326 
 PHE   0.016   0.001   PHE B 208 
 TYR   0.019   0.002   TYR A 299 
 ARG   0.006   0.000   ARG B 382 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 201
  time to evaluate  : 0.749 
Fit side-chains
REVERT: A   40 TYR cc_start: 0.8208 (t80) cc_final: 0.7929 (t80)
REVERT: A   61 PHE cc_start: 0.7103 (m-80) cc_final: 0.6859 (m-80)
REVERT: A  200 LEU cc_start: 0.8504 (mt) cc_final: 0.8031 (mt)
REVERT: A  204 GLU cc_start: 0.5822 (tt0) cc_final: 0.5343 (pt0)
REVERT: A  273 ASP cc_start: 0.7647 (t70) cc_final: 0.7206 (t70)
REVERT: A  330 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8612 (mt)
REVERT: A  381 LEU cc_start: 0.8599 (mt) cc_final: 0.7972 (mt)
REVERT: A  402 SER cc_start: 0.8591 (p) cc_final: 0.7987 (t)
REVERT: B  134 SER cc_start: 0.9091 (m) cc_final: 0.8215 (t)
REVERT: B  240 LYS cc_start: 0.7464 (mttp) cc_final: 0.7171 (mttp)
REVERT: B  246 MET cc_start: 0.7365 (ppp) cc_final: 0.6063 (ppp)
REVERT: B  304 ASN cc_start: 0.8177 (m-40) cc_final: 0.7883 (t0)
REVERT: B  381 LEU cc_start: 0.8720 (mt) cc_final: 0.8052 (mt)
REVERT: B  402 SER cc_start: 0.8683 (p) cc_final: 0.8057 (t)
  outliers start: 23
  outliers final: 19
  residues processed: 214
  average time/residue: 0.1430
  time to fit residues: 42.8921
Evaluate side-chains
  217 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 197
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  218 VAL
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  358 GLU
Chi-restraints excluded: chain B residue  392 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 19 optimal weight:    0.3980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 324 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.155769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.136924 restraints weight = 10060.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.138524 restraints weight = 6992.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.139774 restraints weight = 5499.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.088   6378  Z= 0.226
  Angle     :  0.772  15.810   8704  Z= 0.349
  Chirality :  0.042   0.294   1072
  Planarity :  0.005   0.057   1086
  Dihedral  :  6.450  57.194   1018
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 26.13 %
    Favored  : 71.00 %
  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:  3.20 (0.30), residues: 790
  helix:  2.69 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.16 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 258 
 HIS   0.006   0.001   HIS B 326 
 PHE   0.017   0.001   PHE B  24 
 TYR   0.019   0.002   TYR A 299 
 ARG   0.006   0.000   ARG B 382 

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

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

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1580 Ramachandran restraints generated.
    790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 204
  time to evaluate  : 0.675 
Fit side-chains
REVERT: A   40 TYR cc_start: 0.8221 (t80) cc_final: 0.7936 (t80)
REVERT: A   61 PHE cc_start: 0.7097 (m-80) cc_final: 0.6849 (m-80)
REVERT: A  200 LEU cc_start: 0.8470 (mt) cc_final: 0.7986 (mt)
REVERT: A  204 GLU cc_start: 0.5838 (tt0) cc_final: 0.5306 (pt0)
REVERT: A  273 ASP cc_start: 0.7643 (t70) cc_final: 0.7204 (t70)
REVERT: A  309 ASN cc_start: 0.8421 (m-40) cc_final: 0.7994 (m-40)
REVERT: A  330 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8602 (mt)
REVERT: A  381 LEU cc_start: 0.8613 (mt) cc_final: 0.7988 (mt)
REVERT: A  402 SER cc_start: 0.8614 (p) cc_final: 0.7970 (t)
REVERT: B  134 SER cc_start: 0.9093 (m) cc_final: 0.8069 (t)
REVERT: B  240 LYS cc_start: 0.7441 (mttp) cc_final: 0.7184 (mttp)
REVERT: B  246 MET cc_start: 0.7341 (ppp) cc_final: 0.6228 (ppp)
REVERT: B  304 ASN cc_start: 0.8149 (m-40) cc_final: 0.7921 (t0)
REVERT: B  381 LEU cc_start: 0.8728 (mt) cc_final: 0.8035 (mt)
REVERT: B  402 SER cc_start: 0.8651 (p) cc_final: 0.7972 (t)
  outliers start: 19
  outliers final: 18
  residues processed: 215
  average time/residue: 0.1426
  time to fit residues: 42.9977
Evaluate side-chains
  219 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 200
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 VAL
Chi-restraints excluded: chain A residue   93 SER
Chi-restraints excluded: chain A residue   94 CYS
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  159 GLU
Chi-restraints excluded: chain A residue  195 VAL
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  240 LYS
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  347 LEU
Chi-restraints excluded: chain B residue  350 LEU
Chi-restraints excluded: chain B residue  358 GLU
Chi-restraints excluded: chain B residue  392 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 34 optimal weight:    0.4980
   chunk 32 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 11 optimal weight:    0.5980
   chunk 58 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 324 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.156227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.135341 restraints weight = 10115.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.138833 restraints weight = 6003.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.141124 restraints weight = 4120.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.2751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6378  Z= 0.221
  Angle     :  0.776  15.739   8704  Z= 0.352
  Chirality :  0.043   0.279   1072
  Planarity :  0.005   0.055   1086
  Dihedral  :  6.375  57.849   1018
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 25.98 %
    Favored  : 70.54 %
  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:  3.21 (0.30), residues: 790
  helix:  2.68 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.07 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 258 
 HIS   0.006   0.001   HIS B 326 
 PHE   0.017   0.001   PHE B  24 
 TYR   0.021   0.002   TYR A 299 
 ARG   0.006   0.000   ARG B 382 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1931.53 seconds
wall clock time: 35 minutes 26.97 seconds (2126.97 seconds total)