Starting phenix.real_space_refine
on Tue Mar 11 16:01:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p5j_13200/03_2025/7p5j_13200.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p5j_13200/03_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_13200/03_2025/7p5j_13200.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p5j_13200/03_2025/7p5j_13200.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p5j_13200/03_2025/7p5j_13200.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p5j_13200/03_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-5624/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: 4.06, per 1000 atoms: 0.65
  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: 1.53
  Conformation dependent library (CDL) restraints added in 814.8 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: 0.59
  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: 1.62

  Time building geometry restraints manager: 1.82 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:             0.420
  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:                    0.060
  Process input model:                     17.130
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.930
-------------------------------------------------------------------------------
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  : 0.633 
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: 0.1420
  time to fit residues: 47.3587
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  : 0.671 
-------------------------------------------------------------------------------
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 = 0.153476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.132391 restraints weight = 9925.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.135709 restraints weight = 5993.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.137867 restraints weight = 4159.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
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  : 10.270  73.404   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  : 0.689 
Fit side-chains
REVERT: A   40 TYR cc_start: 0.7956 (t80) cc_final: 0.7743 (t80)
REVERT: A  131 HIS cc_start: 0.8144 (t70) cc_final: 0.7893 (t70)
REVERT: A  273 ASP cc_start: 0.7523 (t70) cc_final: 0.7158 (t70)
REVERT: A  381 LEU cc_start: 0.8650 (mt) cc_final: 0.8428 (mt)
REVERT: B  134 SER cc_start: 0.9013 (m) cc_final: 0.8155 (t)
REVERT: B  304 ASN cc_start: 0.8257 (m-40) cc_final: 0.7738 (m-40)
  outliers start: 16
  outliers final: 11
  residues processed: 224
  average time/residue: 0.1472
  time to fit residues: 45.1781
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  : 0.632 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 53 optimal weight:    0.4980
   chunk 22 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 73 optimal weight:    0.6980
   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 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 = 0.156144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.134885 restraints weight = 10049.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.138375 restraints weight = 6093.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.140839 restraints weight = 4192.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.1824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6378  Z= 0.202
  Angle     :  0.693  10.265   8704  Z= 0.323
  Chirality :  0.041   0.180   1072
  Planarity :  0.005   0.062   1086
  Dihedral  :  8.040  57.530   1018
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 17.82 %
    Favored  : 79.61 %
  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:  3.16 (0.30), residues: 790
  helix:  2.67 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.36 (0.58), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 258 
 HIS   0.005   0.001   HIS B 326 
 PHE   0.036   0.002   PHE B 208 
 TYR   0.027   0.002   TYR A 299 
 ARG   0.002   0.000   ARG A 314 

*********************** 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  : 0.616 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.7919 (t80) cc_final: 0.7663 (t80)
REVERT: A  273 ASP cc_start: 0.7677 (t70) cc_final: 0.7198 (t70)
REVERT: A  381 LEU cc_start: 0.8705 (mt) cc_final: 0.8327 (mt)
REVERT: A  402 SER cc_start: 0.8753 (p) cc_final: 0.8222 (t)
REVERT: B  134 SER cc_start: 0.9001 (m) cc_final: 0.8188 (t)
REVERT: B  214 TRP cc_start: 0.6928 (t60) cc_final: 0.6488 (t60)
REVERT: B  240 LYS cc_start: 0.7600 (mttp) cc_final: 0.7272 (mttp)
REVERT: B  304 ASN cc_start: 0.8202 (m-40) cc_final: 0.7773 (m-40)
REVERT: B  381 LEU cc_start: 0.8593 (mt) cc_final: 0.8214 (mt)
REVERT: B  402 SER cc_start: 0.8686 (p) cc_final: 0.8186 (t)
  outliers start: 17
  outliers final: 13
  residues processed: 220
  average time/residue: 0.1356
  time to fit residues: 41.3295
Evaluate side-chains
  213 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 200
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
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  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:    0.4980
   chunk 77 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0170
   chunk 71 optimal weight:    0.9980
   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:    0.5418

-------------------------------------------------------------------------------
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 = 0.3842 r_free = 0.3842 target = 0.156891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.135757 restraints weight = 10246.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.139359 restraints weight = 6075.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.141791 restraints weight = 4142.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.2053

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= 0.201
  Angle     :  0.691  11.074   8704  Z= 0.317
  Chirality :  0.040   0.216   1072
  Planarity :  0.005   0.060   1086
  Dihedral  :  7.058  55.907   1018
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 19.64 %
    Favored  : 77.04 %
  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:  3.24 (0.30), residues: 790
  helix:  2.75 (0.20), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.44 (0.55), 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   0.028   0.002   PHE B 208 
 TYR   0.017   0.002   TYR A 299 
 ARG   0.001   0.000   ARG A 213 

*********************** 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
  233 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 211
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.7959 (t80) cc_final: 0.7722 (t80)
REVERT: A  273 ASP cc_start: 0.7631 (t70) cc_final: 0.7130 (t70)
REVERT: A  381 LEU cc_start: 0.8653 (mt) cc_final: 0.8305 (mt)
REVERT: A  402 SER cc_start: 0.8692 (p) cc_final: 0.8164 (t)
REVERT: B  134 SER cc_start: 0.8990 (m) cc_final: 0.8111 (t)
REVERT: B  214 TRP cc_start: 0.6744 (t60) cc_final: 0.6462 (t60)
REVERT: B  240 LYS cc_start: 0.7548 (mttp) cc_final: 0.7245 (mttp)
REVERT: B  304 ASN cc_start: 0.8241 (m-40) cc_final: 0.7899 (m-40)
REVERT: B  381 LEU cc_start: 0.8597 (mt) cc_final: 0.8061 (mt)
REVERT: B  402 SER cc_start: 0.8665 (p) cc_final: 0.8165 (t)
  outliers start: 22
  outliers final: 16
  residues processed: 219
  average time/residue: 0.1486
  time to fit residues: 44.8928
Evaluate side-chains
  218 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 202
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
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  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  358 GLU
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:    0.2980
   chunk 77 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   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:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 138 HIS

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 = 0.155752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.134758 restraints weight = 10205.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.138244 restraints weight = 6072.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.140770 restraints weight = 4157.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6378  Z= 0.213
  Angle     :  0.711  13.936   8704  Z= 0.323
  Chirality :  0.040   0.167   1072
  Planarity :  0.005   0.056   1086
  Dihedral  :  6.722  59.348   1018
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 21.15 %
    Favored  : 75.23 %
  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:  3.24 (0.30), residues: 790
  helix:  2.79 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.59 (0.53), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 258 
 HIS   0.009   0.001   HIS B 138 
 PHE   0.016   0.001   PHE B 208 
 TYR   0.017   0.002   TYR A 299 
 ARG   0.002   0.000   ARG A 146 

*********************** 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
  236 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 212
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8087 (t80) cc_final: 0.7735 (t80)
REVERT: A  273 ASP cc_start: 0.7689 (t70) cc_final: 0.7128 (t70)
REVERT: A  381 LEU cc_start: 0.8562 (mt) cc_final: 0.8078 (mt)
REVERT: A  402 SER cc_start: 0.8646 (p) cc_final: 0.8091 (t)
REVERT: B  134 SER cc_start: 0.9041 (m) cc_final: 0.8165 (t)
REVERT: B  240 LYS cc_start: 0.7546 (mttp) cc_final: 0.7275 (mttp)
REVERT: B  246 MET cc_start: 0.7464 (ppp) cc_final: 0.6165 (ppp)
REVERT: B  304 ASN cc_start: 0.8246 (m-40) cc_final: 0.7830 (m-40)
REVERT: B  381 LEU cc_start: 0.8705 (mt) cc_final: 0.8033 (mt)
REVERT: B  402 SER cc_start: 0.8643 (p) cc_final: 0.8139 (t)
  outliers start: 24
  outliers final: 21
  residues processed: 222
  average time/residue: 0.1413
  time to fit residues: 42.9827
Evaluate side-chains
  223 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 202
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
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  211 GLU
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  358 GLU
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:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 57 optimal weight:    0.5980
   chunk 77 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3823 r_free = 0.3823 target = 0.155158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.135466 restraints weight = 10091.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.138544 restraints weight = 6315.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.140710 restraints weight = 4448.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.2380

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= 0.211
  Angle     :  0.733  14.855   8704  Z= 0.329
  Chirality :  0.041   0.221   1072
  Planarity :  0.005   0.052   1086
  Dihedral  :  6.618  58.650   1018
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 22.66 %
    Favored  : 73.41 %
  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:  3.25 (0.30), residues: 790
  helix:  2.77 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.51 (0.54), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 258 
 HIS   0.014   0.001   HIS B 138 
 PHE   0.017   0.001   PHE B 208 
 TYR   0.018   0.002   TYR A 299 
 ARG   0.006   0.000   ARG B 382 

*********************** 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
  227 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 201
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8151 (t80) cc_final: 0.7892 (t80)
REVERT: A  273 ASP cc_start: 0.7732 (t70) cc_final: 0.7138 (t70)
REVERT: A  330 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8635 (mt)
REVERT: A  381 LEU cc_start: 0.8549 (mt) cc_final: 0.7977 (mt)
REVERT: A  402 SER cc_start: 0.8627 (p) cc_final: 0.8150 (t)
REVERT: B  134 SER cc_start: 0.9030 (m) cc_final: 0.8042 (t)
REVERT: B  240 LYS cc_start: 0.7501 (mttp) cc_final: 0.7228 (mttp)
REVERT: B  246 MET cc_start: 0.7281 (ppp) cc_final: 0.5900 (ppp)
REVERT: B  304 ASN cc_start: 0.8238 (m-40) cc_final: 0.7881 (t0)
REVERT: B  381 LEU cc_start: 0.8678 (mt) cc_final: 0.7996 (mt)
REVERT: B  402 SER cc_start: 0.8673 (p) cc_final: 0.8185 (t)
  outliers start: 26
  outliers final: 22
  residues processed: 213
  average time/residue: 0.1336
  time to fit residues: 39.8449
Evaluate side-chains
  218 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 195
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
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  211 GLU
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:    7.9990
   chunk 19 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0370
   chunk 77 optimal weight:    5.9990
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
A  17 HIS
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 138 HIS
B 324 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.155929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.135028 restraints weight = 10017.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.138487 restraints weight = 5969.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.140898 restraints weight = 4107.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   6378  Z= 0.211
  Angle     :  0.754  15.176   8704  Z= 0.340
  Chirality :  0.042   0.301   1072
  Planarity :  0.005   0.051   1086
  Dihedral  :  6.511  58.491   1018
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 24.32 %
    Favored  : 71.75 %
  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:  2.73 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.47 (0.53), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 258 
 HIS   0.011   0.001   HIS B 138 
 PHE   0.017   0.001   PHE B 208 
 TYR   0.021   0.002   TYR A 299 
 ARG   0.005   0.000   ARG B 382 

*********************** 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: 26
    poor density    : 204
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8118 (t80) cc_final: 0.7853 (t80)
REVERT: A   61 PHE cc_start: 0.7328 (m-80) cc_final: 0.7055 (m-80)
REVERT: A  273 ASP cc_start: 0.7684 (t70) cc_final: 0.7237 (t70)
REVERT: A  330 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8584 (mt)
REVERT: A  381 LEU cc_start: 0.8603 (mt) cc_final: 0.8004 (mt)
REVERT: A  402 SER cc_start: 0.8647 (p) cc_final: 0.8126 (t)
REVERT: B  134 SER cc_start: 0.8988 (m) cc_final: 0.7923 (t)
REVERT: B  240 LYS cc_start: 0.7505 (mttp) cc_final: 0.7217 (mttp)
REVERT: B  246 MET cc_start: 0.7159 (ppp) cc_final: 0.5745 (ppp)
REVERT: B  304 ASN cc_start: 0.8138 (m-40) cc_final: 0.7887 (t0)
REVERT: B  381 LEU cc_start: 0.8700 (mt) cc_final: 0.8034 (mt)
REVERT: B  402 SER cc_start: 0.8668 (p) cc_final: 0.8124 (t)
  outliers start: 26
  outliers final: 22
  residues processed: 216
  average time/residue: 0.1405
  time to fit residues: 42.1310
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  : 0.684 
-------------------------------------------------------------------------------
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  211 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.155817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.135132 restraints weight = 9954.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.138497 restraints weight = 5937.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.140867 restraints weight = 4126.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080   6378  Z= 0.222
  Angle     :  0.760  15.596   8704  Z= 0.342
  Chirality :  0.042   0.300   1072
  Planarity :  0.005   0.051   1086
  Dihedral  :  6.407  57.034   1018
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 25.08 %
    Favored  : 71.30 %
  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:  3.25 (0.30), residues: 790
  helix:  2.74 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.33 (0.54), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 258 
 HIS   0.005   0.001   HIS B 326 
 PHE   0.017   0.001   PHE B 208 
 TYR   0.024   0.002   TYR A 299 
 ARG   0.006   0.000   ARG B 177 

*********************** 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
  229 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 205
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8111 (t80) cc_final: 0.7844 (t80)
REVERT: A   61 PHE cc_start: 0.7060 (m-80) cc_final: 0.6804 (m-80)
REVERT: A  273 ASP cc_start: 0.7688 (t70) cc_final: 0.7167 (t70)
REVERT: A  330 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8546 (mt)
REVERT: A  381 LEU cc_start: 0.8602 (mt) cc_final: 0.8011 (mt)
REVERT: A  402 SER cc_start: 0.8628 (p) cc_final: 0.8051 (t)
REVERT: B  134 SER cc_start: 0.9069 (m) cc_final: 0.8172 (t)
REVERT: B  240 LYS cc_start: 0.7466 (mttp) cc_final: 0.7216 (mttp)
REVERT: B  246 MET cc_start: 0.7182 (ppp) cc_final: 0.5752 (ppp)
REVERT: B  304 ASN cc_start: 0.8118 (m-40) cc_final: 0.7909 (t0)
REVERT: B  381 LEU cc_start: 0.8718 (mt) cc_final: 0.8052 (mt)
REVERT: B  402 SER cc_start: 0.8704 (p) cc_final: 0.8092 (t)
  outliers start: 24
  outliers final: 21
  residues processed: 218
  average time/residue: 0.1411
  time to fit residues: 42.6423
Evaluate side-chains
  222 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 200
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
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  211 GLU
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 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:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0670
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.156462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.135855 restraints weight = 10046.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.139289 restraints weight = 5980.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.141748 restraints weight = 4114.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.084   6378  Z= 0.220
  Angle     :  0.776  15.482   8704  Z= 0.351
  Chirality :  0.042   0.266   1072
  Planarity :  0.005   0.056   1086
  Dihedral  :  6.371  57.264   1018
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 25.83 %
    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:  3.27 (0.30), residues: 790
  helix:  2.73 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.18 (0.55), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 258 
 HIS   0.005   0.001   HIS B 326 
 PHE   0.016   0.001   PHE B 208 
 TYR   0.023   0.001   TYR A 299 
 ARG   0.005   0.000   ARG A 177 

*********************** 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: 24
    poor density    : 200
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8122 (t80) cc_final: 0.7869 (t80)
REVERT: A   61 PHE cc_start: 0.7065 (m-80) cc_final: 0.6820 (m-80)
REVERT: A  204 GLU cc_start: 0.5878 (tt0) cc_final: 0.5522 (pt0)
REVERT: A  273 ASP cc_start: 0.7760 (t70) cc_final: 0.7246 (t70)
REVERT: A  330 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8566 (mt)
REVERT: A  381 LEU cc_start: 0.8573 (mt) cc_final: 0.7953 (mt)
REVERT: A  402 SER cc_start: 0.8630 (p) cc_final: 0.8058 (t)
REVERT: B  134 SER cc_start: 0.9047 (m) cc_final: 0.8136 (t)
REVERT: B  240 LYS cc_start: 0.7448 (mttp) cc_final: 0.7149 (mttp)
REVERT: B  246 MET cc_start: 0.7196 (ppp) cc_final: 0.5821 (ppp)
REVERT: B  381 LEU cc_start: 0.8697 (mt) cc_final: 0.8026 (mt)
REVERT: B  402 SER cc_start: 0.8728 (p) cc_final: 0.8108 (t)
  outliers start: 24
  outliers final: 20
  residues processed: 213
  average time/residue: 0.1292
  time to fit residues: 38.6539
Evaluate side-chains
  213 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 192
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
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  211 GLU
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:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 38 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0040
   chunk 16 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.157127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.136224 restraints weight = 10008.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.139725 restraints weight = 5960.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.142010 restraints weight = 4101.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.087   6378  Z= 0.214
  Angle     :  0.781  15.387   8704  Z= 0.353
  Chirality :  0.043   0.291   1072
  Planarity :  0.005   0.054   1086
  Dihedral  :  6.278  55.612   1018
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 25.53 %
    Favored  : 71.30 %
  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:  3.22 (0.29), residues: 790
  helix:  2.70 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop : -1.22 (0.53), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 258 
 HIS   0.005   0.001   HIS B 326 
 PHE   0.015   0.001   PHE B  24 
 TYR   0.024   0.002   TYR A 299 
 ARG   0.004   0.000   ARG A 177 

********************** 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
  221 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 200
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 TYR cc_start: 0.8146 (t80) cc_final: 0.7879 (t80)
REVERT: A   61 PHE cc_start: 0.7070 (m-80) cc_final: 0.6819 (m-80)
REVERT: A  204 GLU cc_start: 0.5861 (tt0) cc_final: 0.5476 (pt0)
REVERT: A  273 ASP cc_start: 0.7698 (t70) cc_final: 0.7172 (t70)
REVERT: A  330 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8559 (mt)
REVERT: A  381 LEU cc_start: 0.8578 (mt) cc_final: 0.7950 (mt)
REVERT: A  402 SER cc_start: 0.8624 (p) cc_final: 0.7998 (t)
REVERT: B  134 SER cc_start: 0.9023 (m) cc_final: 0.8096 (t)
REVERT: B  240 LYS cc_start: 0.7444 (mttp) cc_final: 0.7156 (mttp)
REVERT: B  246 MET cc_start: 0.7217 (ppp) cc_final: 0.6088 (ppp)
REVERT: B  381 LEU cc_start: 0.8712 (mt) cc_final: 0.8028 (mt)
REVERT: B  402 SER cc_start: 0.8709 (p) cc_final: 0.8045 (t)
  outliers start: 21
  outliers final: 20
  residues processed: 212
  average time/residue: 0.1361
  time to fit residues: 40.1233
Evaluate side-chains
  218 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 197
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
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  211 GLU
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 48 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 11 optimal weight:    0.3980
   chunk 58 optimal weight:    0.8980
   chunk 56 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.156061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.137075 restraints weight = 10152.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.138668 restraints weight = 6920.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.140131 restraints weight = 5347.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6378  Z= 0.218
  Angle     :  0.788  16.447   8704  Z= 0.356
  Chirality :  0.043   0.282   1072
  Planarity :  0.005   0.055   1086
  Dihedral  :  6.259  55.430   1018
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 26.13 %
    Favored  : 70.39 %
  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:  3.21 (0.30), residues: 790
  helix:  2.70 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop : -1.22 (0.55), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 258 
 HIS   0.005   0.001   HIS B 326 
 PHE   0.015   0.001   PHE B 208 
 TYR   0.024   0.002   TYR A 299 
 ARG   0.004   0.000   ARG A 177 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1949.47 seconds
wall clock time: 34 minutes 36.09 seconds (2076.09 seconds total)