Starting phenix.real_space_refine
on Sun May 11 05:47:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k66_36918/05_2025/8k66_36918.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k66_36918/05_2025/8k66_36918.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k66_36918/05_2025/8k66_36918.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k66_36918/05_2025/8k66_36918.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k66_36918/05_2025/8k66_36918.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k66_36918/05_2025/8k66_36918.cif"
  }
  resolution = 2.53
  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=   0.001
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      34      5.16       5
     Na      4      4.78       5
     C    5070      2.51       5
     N    1120      2.21       5
     O    1386      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7620
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3514
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 443, 3511
          Classifications: {'peptide': 443}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 424}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 443, 3511
          Classifications: {'peptide': 443}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 424}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 3595
    Chain: "B"
      Number of atoms: 3514
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 443, 3511
          Classifications: {'peptide': 443}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 424}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 443, 3511
          Classifications: {'peptide': 443}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 424}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 3595
    Chain: "A"
      Number of atoms: 231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 231
          Unusual residues: {' NA': 2, 'CLR': 1, 'PC1': 1, 'PTY': 1, 'T7X': 1, 'Y01': 2}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'T7X:plan-5': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 231
          Unusual residues: {' NA': 2, 'CLR': 1, 'PC1': 1, 'PTY': 1, 'T7X': 1, 'Y01': 2}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'T7X:plan-5': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 65
          Classifications: {'water': 65}
          Link IDs: {None: 64}
    Chain: "B"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 65
          Classifications: {'water': 65}
          Link IDs: {None: 64}
  Time building chain proxies: 9.46, per 1000 atoms: 1.24
  Number of scatterers: 7620
  At special positions: 0
  Unit cell: (104.498, 110.423, 82.4135, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      34     16.00
     P       6     15.00
     Na      4     11.00
     O    1386      8.00
     N    1120      7.00
     C    5070      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 476 " - pdb=" SG ACYS A 488 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 476 " - pdb=" SG ACYS B 488 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.06
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1668

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 2 sheets defined
      77.7% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 38
      removed outlier: 3.803A  pdb=" N   PHE A  26 " --> pdb=" O   TYR A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 62
    Processing helix  chain 'A' and resid 72 through 85
    Processing helix  chain 'A' and resid 98 through 113
    Processing helix  chain 'A' and resid 113 through 125
    Processing helix  chain 'A' and resid 181 through 214
    Processing helix  chain 'A' and resid 214 through 225
      Proline residue:  A 220  - end of helix
    Processing helix  chain 'A' and resid 227 through 241
    Processing helix  chain 'A' and resid 252 through 256
    Processing helix  chain 'A' and resid 258 through 273
    Processing helix  chain 'A' and resid 275 through 292
    Processing helix  chain 'A' and resid 293 through 301
      removed outlier: 3.684A  pdb=" N   LYS A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 306
      removed outlier: 3.608A  pdb=" N   GLU A 305 " --> pdb=" O   ASN A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 340
    Processing helix  chain 'A' and resid 342 through 346
    Processing helix  chain 'A' and resid 349 through 364
    Processing helix  chain 'A' and resid 373 through 377
    Processing helix  chain 'A' and resid 378 through 391
      removed outlier: 3.564A  pdb=" N   LEU A 384 " --> pdb=" O   ALA A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 423
    Processing helix  chain 'A' and resid 425 through 441
    Processing helix  chain 'A' and resid 441 through 448
    Processing helix  chain 'A' and resid 453 through 466
    Processing helix  chain 'A' and resid 475 through 481
      removed outlier: 3.535A  pdb=" N   LEU A 479 " --> pdb=" O   SER A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 499
    Processing helix  chain 'A' and resid 500 through 516
      removed outlier: 3.552A  pdb=" N   LEU A 516 " --> pdb=" O   LEU A 512 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 38
    Processing helix  chain 'B' and resid 39 through 62
    Processing helix  chain 'B' and resid 72 through 85
    Processing helix  chain 'B' and resid 93 through 97
    Processing helix  chain 'B' and resid 98 through 113
    Processing helix  chain 'B' and resid 113 through 125
    Processing helix  chain 'B' and resid 181 through 214
    Processing helix  chain 'B' and resid 214 through 225
      Proline residue:  B 220  - end of helix
    Processing helix  chain 'B' and resid 227 through 241
    Processing helix  chain 'B' and resid 252 through 256
    Processing helix  chain 'B' and resid 258 through 273
    Processing helix  chain 'B' and resid 275 through 292
    Processing helix  chain 'B' and resid 293 through 302
      removed outlier: 3.599A  pdb=" N   LYS B 297 " --> pdb=" O   LEU B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 340
    Processing helix  chain 'B' and resid 342 through 346
    Processing helix  chain 'B' and resid 349 through 364
    Processing helix  chain 'B' and resid 373 through 377
    Processing helix  chain 'B' and resid 378 through 391
      removed outlier: 3.535A  pdb=" N   LEU B 384 " --> pdb=" O   ALA B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 423
    Processing helix  chain 'B' and resid 425 through 441
    Processing helix  chain 'B' and resid 441 through 448
    Processing helix  chain 'B' and resid 453 through 466
    Processing helix  chain 'B' and resid 475 through 481
      removed outlier: 3.533A  pdb=" N   LEU B 479 " --> pdb=" O   SER B 475 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 499
    Processing helix  chain 'B' and resid 500 through 516
      removed outlier: 3.550A  pdb=" N   LEU B 516 " --> pdb=" O   LEU B 512 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 397
    Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 528

    486 hydrogen bonds defined for protein.
    1389 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: 2.00

  Time building geometry restraints manager: 2.23 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1052
        1.31 -     1.44: 2090
        1.44 -     1.57: 4466
        1.57 -     1.71: 12
        1.71 -     1.84: 58
  Bond restraints: 7678
  Sorted by residual:
  bond pdb=" CA  SER A  87 "
       pdb=" CB  SER A  87 "
    ideal  model  delta    sigma   weight residual
    1.531  1.461  0.070 1.56e-02 4.11e+03 2.04e+01
  bond pdb=" CA  SER B  87 "
       pdb=" CB  SER B  87 "
    ideal  model  delta    sigma   weight residual
    1.531  1.462  0.070 1.56e-02 4.11e+03 1.99e+01
  bond pdb=" C11 T7X B 704 "
       pdb=" O18 T7X B 704 "
    ideal  model  delta    sigma   weight residual
    1.327  1.400 -0.073 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" C11 T7X A 603 "
       pdb=" O18 T7X A 603 "
    ideal  model  delta    sigma   weight residual
    1.327  1.400 -0.073 2.00e-02 2.50e+03 1.33e+01
  bond pdb=" N   ILE A  90 "
       pdb=" CA  ILE A  90 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.039 1.14e-02 7.69e+03 1.16e+01
  ... (remaining 7673 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.20: 10176
        3.20 -     6.40: 208
        6.40 -     9.60: 28
        9.60 -    12.80: 2
       12.80 -    15.99: 6
  Bond angle restraints: 10420
  Sorted by residual:
  angle pdb=" O1  T7X B 704 "
        pdb=" P1  T7X B 704 "
        pdb=" O13 T7X B 704 "
      ideal   model   delta    sigma   weight residual
      94.60  110.59  -15.99 3.00e+00 1.11e-01 2.84e+01
  angle pdb=" O1  T7X A 603 "
        pdb=" P1  T7X A 603 "
        pdb=" O13 T7X A 603 "
      ideal   model   delta    sigma   weight residual
      94.60  110.57  -15.97 3.00e+00 1.11e-01 2.83e+01
  angle pdb=" O11 PTY B 705 "
        pdb=" P1  PTY B 705 "
        pdb=" O14 PTY B 705 "
      ideal   model   delta    sigma   weight residual
      92.90  108.67  -15.77 3.00e+00 1.11e-01 2.76e+01
  angle pdb=" O11 PTY A 604 "
        pdb=" P1  PTY A 604 "
        pdb=" O14 PTY A 604 "
      ideal   model   delta    sigma   weight residual
      92.90  108.64  -15.74 3.00e+00 1.11e-01 2.75e+01
  angle pdb=" O12 PC1 B 701 "
        pdb=" P   PC1 B 701 "
        pdb=" O14 PC1 B 701 "
      ideal   model   delta    sigma   weight residual
     123.67  110.29   13.38 3.00e+00 1.11e-01 1.99e+01
  ... (remaining 10415 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.32: 4594
       32.32 -    64.63: 248
       64.63 -    96.95: 35
       96.95 -   129.27: 11
      129.27 -   161.58: 2
  Dihedral angle restraints: 4890
    sinusoidal: 2308
      harmonic: 2582
  Sorted by residual:
  dihedral pdb=" C9  T7X B 704 "
           pdb=" C7  T7X B 704 "
           pdb=" C8  T7X B 704 "
           pdb=" O13 T7X B 704 "
      ideal   model   delta sinusoidal    sigma   weight residual
      64.16 -134.26 -161.58     1      3.00e+01 1.11e-03 2.08e+01
  dihedral pdb=" C9  T7X A 603 "
           pdb=" C7  T7X A 603 "
           pdb=" C8  T7X A 603 "
           pdb=" O13 T7X A 603 "
      ideal   model   delta sinusoidal    sigma   weight residual
      64.16 -134.27 -161.57     1      3.00e+01 1.11e-03 2.08e+01
  dihedral pdb=" CA  ILE A 300 "
           pdb=" C   ILE A 300 "
           pdb=" N   LYS A 301 "
           pdb=" CA  LYS A 301 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.76   21.24     0      5.00e+00 4.00e-02 1.80e+01
  ... (remaining 4887 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.957: 1226
       0.957 -    1.914: 0
       1.914 -    2.871: 0
       2.871 -    3.827: 0
       3.827 -    4.784: 2
  Chirality restraints: 1228
  Sorted by residual:
  chirality pdb=" C1  T7X B 704 "
            pdb=" C2  T7X B 704 "
            pdb=" C6  T7X B 704 "
            pdb=" O1  T7X B 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42    2.37   -4.78 2.00e-01 2.50e+01 5.72e+02
  chirality pdb=" C1  T7X A 603 "
            pdb=" C2  T7X A 603 "
            pdb=" C6  T7X A 603 "
            pdb=" O1  T7X A 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42    2.36   -4.78 2.00e-01 2.50e+01 5.72e+02
  chirality pdb=" CBG Y01 B 702 "
            pdb=" CAQ Y01 B 702 "
            pdb=" CBD Y01 B 702 "
            pdb=" CBI Y01 B 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.65    0.32 2.00e-01 2.50e+01 2.52e+00
  ... (remaining 1225 not shown)

  Planarity restraints: 1202
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 249 "   -0.012 2.00e-02 2.50e+03   2.43e-02 5.89e+00
        pdb=" C   ASN B 249 "    0.042 2.00e-02 2.50e+03
        pdb=" O   ASN B 249 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   GLU B 250 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 246 "   -0.030 5.00e-02 4.00e+02   4.54e-02 3.29e+00
        pdb=" N   PRO B 247 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B 247 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 247 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 246 "    0.025 5.00e-02 4.00e+02   3.75e-02 2.25e+00
        pdb=" N   PRO A 247 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 247 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 247 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1199 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 85
        2.58 -     3.16: 6031
        3.16 -     3.74: 12201
        3.74 -     4.32: 18197
        4.32 -     4.90: 29062
  Nonbonded interactions: 65576
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 478 "
            pdb=" O   HOH A 701 "
     model   vdw
     1.997 3.120
  nonbonded pdb=" O   LEU A 245 "
            pdb=" O   HOH A 702 "
     model   vdw
     2.011 3.040
  nonbonded pdb=" O   LEU B  86 "
            pdb="NA    NA B 707 "
     model   vdw
     2.027 2.470
  nonbonded pdb=" O   HOH A 750 "
            pdb=" O   HOH A 762 "
     model   vdw
     2.039 3.040
  nonbonded pdb=" O   HOH B 819 "
            pdb=" O   HOH B 860 "
     model   vdw
     2.042 3.040
  ... (remaining 65571 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' and (resid 22 through 487 or resid 489 through 530 or resid 602 or re \ 
sid 607 through 608))
  selection = (chain 'B' and (resid 22 through 487 or resid 489 through 530 or resid 702 or re \ 
sid 707 through 708))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.580
  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:          0.410
  Check model and map are aligned:         0.050
  Set scattering table:                    0.090
  Process input model:                     25.040
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.040
  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:11.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   42.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
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      :  0.006   0.073   7680  Z= 0.305
  Angle     :  1.051  15.995  10424  Z= 0.469
  Chirality :  0.199   4.784   1228
  Planarity :  0.004   0.045   1202
  Dihedral  : 19.607 161.581   3216
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 13.68 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.26), residues: 876
  helix:  0.39 (0.19), residues: 626
  sheet:  None (None), residues: 0
  loop : -1.86 (0.35), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 285 
 HIS   0.002   0.001   HIS B 200 
 PHE   0.013   0.001   PHE B 196 
 TYR   0.015   0.002   TYR B 195 
 ARG   0.005   0.001   ARG A 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13957 (  486)
  hydrogen bonds       : angle       4.67253 ( 1389)
  SS BOND              : bond        0.01487 (    2)
  SS BOND              : angle       2.95067 (    4)
  covalent geometry    : bond        0.00589 ( 7678)
  covalent geometry    : angle       1.04941 (10420)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.764 
Fit side-chains
REVERT: A   61 PHE cc_start: 0.7266 (m-10) cc_final: 0.6881 (m-80)
REVERT: A   63 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7480 (mmpt)
REVERT: A  185 ARG cc_start: 0.7666 (ttp-170) cc_final: 0.7234 (ttm-80)
REVERT: A  304 GLU cc_start: 0.7311 (pm20) cc_final: 0.6992 (mp0)
REVERT: A  414 LYS cc_start: 0.6306 (OUTLIER) cc_final: 0.6036 (tptp)
REVERT: A  422 LEU cc_start: 0.8354 (tp) cc_final: 0.8146 (tp)
REVERT: B   70 ARG cc_start: 0.6811 (mtm-85) cc_final: 0.6486 (mpp-170)
REVERT: B  185 ARG cc_start: 0.7710 (ttp-170) cc_final: 0.7343 (ttm-80)
REVERT: B  422 LEU cc_start: 0.8354 (tp) cc_final: 0.8137 (tp)
  outliers start: 25
  outliers final: 9
  residues processed: 141
  average time/residue: 1.4217
  time to fit residues: 210.2461
Evaluate side-chains
  115 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 LYS
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  414 LYS
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain B residue   63 LYS
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  415 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 44 optimal weight:    7.9990
   chunk 35 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A  25 ASN
A  39 HIS
A 200 HIS
A 273 ASN
A 421 ASN
A 483 HIS
B  25 ASN
B  31 HIS
B  39 HIS
B 200 HIS
B 273 ASN
B 421 ASN
B 483 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.122211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.094526 restraints weight = 8754.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 1.29
r_work: 0.2786 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2670 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2683
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2683
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.1112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   7680  Z= 0.152
  Angle     :  0.579   6.735  10424  Z= 0.298
  Chirality :  0.040   0.130   1228
  Planarity :  0.005   0.041   1202
  Dihedral  : 15.007 157.189   1641
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 14.58 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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:  1.29 (0.28), residues: 876
  helix:  1.59 (0.20), residues: 632
  sheet:  None (None), residues: 0
  loop : -1.07 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  42 
 HIS   0.003   0.001   HIS A 483 
 PHE   0.013   0.001   PHE B 196 
 TYR   0.016   0.002   TYR B 195 
 ARG   0.006   0.001   ARG B 528 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04847 (  486)
  hydrogen bonds       : angle       3.86280 ( 1389)
  SS BOND              : bond        0.01383 (    2)
  SS BOND              : angle       2.87304 (    4)
  covalent geometry    : bond        0.00351 ( 7678)
  covalent geometry    : angle       0.57629 (10420)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.821 
Fit side-chains
REVERT: A   61 PHE cc_start: 0.7740 (m-10) cc_final: 0.7332 (m-80)
REVERT: A   68 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6984 (mm-30)
REVERT: A  185 ARG cc_start: 0.7815 (ttp-170) cc_final: 0.6969 (ttm-80)
REVERT: A  213 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7283 (mmt180)
REVERT: A  304 GLU cc_start: 0.7096 (pm20) cc_final: 0.6747 (mp0)
REVERT: A  422 LEU cc_start: 0.8264 (tp) cc_final: 0.8059 (tp)
REVERT: A  529 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9012 (mp)
REVERT: B   70 ARG cc_start: 0.7152 (mtm-85) cc_final: 0.6939 (mpp80)
REVERT: B  185 ARG cc_start: 0.7747 (ttp-170) cc_final: 0.7023 (ttm-80)
REVERT: B  422 LEU cc_start: 0.8315 (tp) cc_final: 0.8094 (tp)
REVERT: B  529 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9023 (mp)
  outliers start: 21
  outliers final: 13
  residues processed: 120
  average time/residue: 1.2814
  time to fit residues: 162.6093
Evaluate side-chains
  113 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  213 ARG
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  486 SER
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  304 GLU
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  486 SER
Chi-restraints excluded: chain B residue  529 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 87 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 421 ASN
B 421 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.124931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.096217 restraints weight = 12202.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 1.51
r_work: 0.2787 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2667 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2653
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2653 r_free = 0.2653    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2653 r_free = 0.2653    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2653
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7680  Z= 0.119
  Angle     :  0.518   5.667  10424  Z= 0.270
  Chirality :  0.038   0.128   1228
  Planarity :  0.004   0.041   1202
  Dihedral  : 13.979 154.784   1626
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 14.96 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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:  1.94 (0.29), residues: 876
  helix:  2.04 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.83 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 285 
 HIS   0.002   0.001   HIS A  39 
 PHE   0.013   0.001   PHE B 196 
 TYR   0.015   0.002   TYR A 195 
 ARG   0.009   0.001   ARG B 528 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04138 (  486)
  hydrogen bonds       : angle       3.67919 ( 1389)
  SS BOND              : bond        0.01317 (    2)
  SS BOND              : angle       2.82618 (    4)
  covalent geometry    : bond        0.00264 ( 7678)
  covalent geometry    : angle       0.51557 (10420)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.861 
Fit side-chains
REVERT: A   61 PHE cc_start: 0.7680 (m-10) cc_final: 0.7199 (m-80)
REVERT: A   68 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6975 (mm-30)
REVERT: A   70 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.7115 (ptp90)
REVERT: A  185 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.6959 (ttm-80)
REVERT: A  304 GLU cc_start: 0.7114 (pm20) cc_final: 0.6767 (mp0)
REVERT: A  422 LEU cc_start: 0.8306 (tp) cc_final: 0.8091 (tp)
REVERT: A  478 ARG cc_start: 0.8143 (mtp180) cc_final: 0.7724 (mtm180)
REVERT: A  529 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9029 (mp)
REVERT: B  185 ARG cc_start: 0.7805 (ttp-170) cc_final: 0.7059 (ttm-80)
REVERT: B  422 LEU cc_start: 0.8319 (tp) cc_final: 0.8101 (tp)
REVERT: B  529 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9039 (mp)
  outliers start: 19
  outliers final: 7
  residues processed: 119
  average time/residue: 1.3156
  time to fit residues: 165.0324
Evaluate side-chains
  113 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue   70 ARG
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  234 SER
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  529 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 84 optimal weight:    0.2980
   chunk 85 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 421 ASN
B 421 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.123570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.095960 restraints weight = 9173.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.2923 rms_B_bonded: 1.31
r_work: 0.2810 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2694 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2682
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2682 r_free = 0.2682    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2682 r_free = 0.2682    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2682
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8733
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7680  Z= 0.119
  Angle     :  0.516   5.287  10424  Z= 0.269
  Chirality :  0.038   0.127   1228
  Planarity :  0.004   0.040   1202
  Dihedral  : 13.414 149.892   1620
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 15.35 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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:  2.16 (0.29), residues: 876
  helix:  2.21 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.74 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 285 
 HIS   0.002   0.001   HIS A 200 
 PHE   0.013   0.001   PHE B 196 
 TYR   0.015   0.002   TYR A 195 
 ARG   0.011   0.001   ARG B 528 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04065 (  486)
  hydrogen bonds       : angle       3.59706 ( 1389)
  SS BOND              : bond        0.01301 (    2)
  SS BOND              : angle       2.94164 (    4)
  covalent geometry    : bond        0.00264 ( 7678)
  covalent geometry    : angle       0.51241 (10420)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.779 
Fit side-chains
REVERT: A   61 PHE cc_start: 0.7624 (m-10) cc_final: 0.7114 (m-80)
REVERT: A   68 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6949 (mm-30)
REVERT: A   70 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.7117 (ptp90)
REVERT: A  185 ARG cc_start: 0.7817 (ttp-170) cc_final: 0.6952 (ttm-80)
REVERT: A  304 GLU cc_start: 0.7102 (pm20) cc_final: 0.6717 (mp0)
REVERT: A  422 LEU cc_start: 0.8288 (tp) cc_final: 0.8067 (tp)
REVERT: A  478 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7691 (mtm180)
REVERT: A  486 SER cc_start: 0.7469 (OUTLIER) cc_final: 0.7101 (p)
REVERT: A  529 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9039 (mp)
REVERT: B   65 SER cc_start: 0.7803 (m) cc_final: 0.7543 (p)
REVERT: B  185 ARG cc_start: 0.7777 (ttp-170) cc_final: 0.7054 (ttm-80)
REVERT: B  422 LEU cc_start: 0.8269 (tp) cc_final: 0.8048 (tp)
REVERT: B  486 SER cc_start: 0.7497 (OUTLIER) cc_final: 0.7098 (p)
REVERT: B  529 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9045 (mp)
  outliers start: 17
  outliers final: 8
  residues processed: 117
  average time/residue: 1.3640
  time to fit residues: 168.0336
Evaluate side-chains
  115 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue   70 ARG
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  234 SER
Chi-restraints excluded: chain A residue  486 SER
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  304 GLU
Chi-restraints excluded: chain B residue  486 SER
Chi-restraints excluded: chain B residue  529 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 421 ASN
B 421 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.121542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.094588 restraints weight = 9321.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 1.30
r_work: 0.2750 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2633 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2625 r_free = 0.2625    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.1399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   7680  Z= 0.192
  Angle     :  0.618   5.712  10424  Z= 0.318
  Chirality :  0.042   0.144   1228
  Planarity :  0.005   0.043   1202
  Dihedral  : 13.622 128.409   1620
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 15.73 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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:  1.78 (0.28), residues: 876
  helix:  1.94 (0.20), residues: 634
  sheet:  None (None), residues: 0
  loop : -0.89 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A  42 
 HIS   0.003   0.001   HIS A 200 
 PHE   0.014   0.002   PHE B 196 
 TYR   0.017   0.002   TYR A 195 
 ARG   0.010   0.001   ARG B 528 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05267 (  486)
  hydrogen bonds       : angle       3.76666 ( 1389)
  SS BOND              : bond        0.01453 (    2)
  SS BOND              : angle       3.42207 (    4)
  covalent geometry    : bond        0.00458 ( 7678)
  covalent geometry    : angle       0.61425 (10420)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.921 
Fit side-chains
REVERT: A   61 PHE cc_start: 0.7686 (m-10) cc_final: 0.7278 (m-80)
REVERT: A   68 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6986 (mm-30)
REVERT: A   70 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7170 (ptp90)
REVERT: A  185 ARG cc_start: 0.7811 (ttp-170) cc_final: 0.6972 (ttm-80)
REVERT: A  304 GLU cc_start: 0.7136 (pm20) cc_final: 0.6783 (mp0)
REVERT: A  478 ARG cc_start: 0.8141 (mtp180) cc_final: 0.7665 (mtm180)
REVERT: A  529 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8985 (mp)
REVERT: B  185 ARG cc_start: 0.7773 (ttp-170) cc_final: 0.7024 (ttm-80)
REVERT: B  529 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8983 (mp)
  outliers start: 16
  outliers final: 8
  residues processed: 114
  average time/residue: 1.3341
  time to fit residues: 160.2821
Evaluate side-chains
  110 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue   70 ARG
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  300 ILE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  529 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 85 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 73 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 421 ASN
B 421 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.123660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.096847 restraints weight = 8753.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 1.27
r_work: 0.2844 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2731 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2687
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2687 r_free = 0.2687    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2687 r_free = 0.2687    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2687
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8739
moved from start:          0.1536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7680  Z= 0.119
  Angle     :  0.517   5.296  10424  Z= 0.270
  Chirality :  0.038   0.126   1228
  Planarity :  0.004   0.039   1202
  Dihedral  : 13.054 124.167   1620
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 15.73 %
    Favored  : 81.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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:  2.18 (0.29), residues: 876
  helix:  2.23 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.75 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 285 
 HIS   0.002   0.000   HIS A 200 
 PHE   0.013   0.001   PHE B 196 
 TYR   0.015   0.002   TYR B 195 
 ARG   0.010   0.001   ARG A 528 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03989 (  486)
  hydrogen bonds       : angle       3.59813 ( 1389)
  SS BOND              : bond        0.01243 (    2)
  SS BOND              : angle       2.91929 (    4)
  covalent geometry    : bond        0.00266 ( 7678)
  covalent geometry    : angle       0.51438 (10420)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A   61 PHE cc_start: 0.7656 (m-10) cc_final: 0.7169 (m-80)
REVERT: A   68 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.7002 (mm-30)
REVERT: A   70 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7140 (ptp90)
REVERT: A  185 ARG cc_start: 0.7835 (ttp-170) cc_final: 0.7011 (ttm-80)
REVERT: A  304 GLU cc_start: 0.7171 (pm20) cc_final: 0.6796 (mp0)
REVERT: A  414 LYS cc_start: 0.6008 (OUTLIER) cc_final: 0.5705 (tppp)
REVERT: A  422 LEU cc_start: 0.8325 (tp) cc_final: 0.8121 (tp)
REVERT: A  478 ARG cc_start: 0.8147 (mtp180) cc_final: 0.7711 (mtm180)
REVERT: A  529 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9035 (mp)
REVERT: B   65 SER cc_start: 0.7827 (m) cc_final: 0.7619 (p)
REVERT: B  185 ARG cc_start: 0.7796 (ttp-170) cc_final: 0.7087 (ttm-80)
REVERT: B  529 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9063 (mp)
  outliers start: 17
  outliers final: 7
  residues processed: 117
  average time/residue: 1.2675
  time to fit residues: 156.4402
Evaluate side-chains
  112 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue   70 ARG
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  414 LYS
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  529 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 75 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 421 ASN
B 421 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.119616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.092305 restraints weight = 8080.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 1.27
r_work: 0.2830 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2716 rms_B_bonded: 3.31 restraints_weight: 0.2500
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2660
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2660 r_free = 0.2660    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2660 r_free = 0.2660    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2660
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8750
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7680  Z= 0.148
  Angle     :  0.566   6.226  10424  Z= 0.294
  Chirality :  0.040   0.136   1228
  Planarity :  0.004   0.041   1202
  Dihedral  : 13.073 115.239   1620
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.37 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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:  2.06 (0.28), residues: 876
  helix:  2.15 (0.20), residues: 634
  sheet:  None (None), residues: 0
  loop : -0.79 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  42 
 HIS   0.002   0.001   HIS A 200 
 PHE   0.014   0.001   PHE B 196 
 TYR   0.016   0.002   TYR A 195 
 ARG   0.011   0.001   ARG B 528 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04589 (  486)
  hydrogen bonds       : angle       3.66650 ( 1389)
  SS BOND              : bond        0.01292 (    2)
  SS BOND              : angle       3.15064 (    4)
  covalent geometry    : bond        0.00344 ( 7678)
  covalent geometry    : angle       0.56229 (10420)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.819 
Fit side-chains
REVERT: A   61 PHE cc_start: 0.7695 (m-10) cc_final: 0.7225 (m-80)
REVERT: A   68 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.7008 (mm-30)
REVERT: A   70 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7174 (ptp90)
REVERT: A  185 ARG cc_start: 0.7837 (ttp-170) cc_final: 0.7039 (ttm-80)
REVERT: A  304 GLU cc_start: 0.7186 (pm20) cc_final: 0.6786 (mp0)
REVERT: A  414 LYS cc_start: 0.6008 (OUTLIER) cc_final: 0.5685 (tppp)
REVERT: A  478 ARG cc_start: 0.8154 (mtp180) cc_final: 0.7690 (mtm180)
REVERT: A  529 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9016 (mp)
REVERT: B   65 SER cc_start: 0.7837 (m) cc_final: 0.7616 (p)
REVERT: B  185 ARG cc_start: 0.7792 (ttp-170) cc_final: 0.7082 (ttm-80)
REVERT: B  529 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9015 (mp)
  outliers start: 15
  outliers final: 9
  residues processed: 115
  average time/residue: 1.3348
  time to fit residues: 161.8137
Evaluate side-chains
  115 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue   70 ARG
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  414 LYS
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue   82 SER
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  215 SER
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  529 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 84 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 420 GLN
A 421 ASN
B 421 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.121785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.094366 restraints weight = 8315.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.2957 rms_B_bonded: 1.29
r_work: 0.2849 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2735 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2689
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2689 r_free = 0.2689    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2689 r_free = 0.2689    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2689
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.1645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7680  Z= 0.114
  Angle     :  0.512   5.285  10424  Z= 0.268
  Chirality :  0.038   0.126   1228
  Planarity :  0.004   0.039   1202
  Dihedral  : 12.789 118.527   1620
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.62 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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:  2.29 (0.29), residues: 876
  helix:  2.30 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.70 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 285 
 HIS   0.002   0.000   HIS A 200 
 PHE   0.013   0.001   PHE B 196 
 TYR   0.015   0.002   TYR B 195 
 ARG   0.011   0.001   ARG B 528 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03888 (  486)
  hydrogen bonds       : angle       3.57061 ( 1389)
  SS BOND              : bond        0.01213 (    2)
  SS BOND              : angle       2.90203 (    4)
  covalent geometry    : bond        0.00252 ( 7678)
  covalent geometry    : angle       0.50925 (10420)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.755 
Fit side-chains
REVERT: A   61 PHE cc_start: 0.7612 (m-10) cc_final: 0.7077 (m-80)
REVERT: A   68 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6988 (mm-30)
REVERT: A   70 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7132 (ptp90)
REVERT: A  185 ARG cc_start: 0.7819 (ttp-170) cc_final: 0.7013 (ttm-80)
REVERT: A  304 GLU cc_start: 0.7198 (pm20) cc_final: 0.6805 (mp0)
REVERT: A  478 ARG cc_start: 0.8138 (mtp180) cc_final: 0.7685 (mtm180)
REVERT: A  529 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9029 (mp)
REVERT: B   65 SER cc_start: 0.7785 (OUTLIER) cc_final: 0.7575 (p)
REVERT: B  185 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7056 (ttm-80)
REVERT: B  295 GLU cc_start: 0.8097 (mp0) cc_final: 0.7787 (mp0)
REVERT: B  529 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9038 (mp)
  outliers start: 13
  outliers final: 7
  residues processed: 112
  average time/residue: 1.2731
  time to fit residues: 150.5265
Evaluate side-chains
  113 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue   70 ARG
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  529 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0020
   chunk 7 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   overall best weight:    0.6388

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

Flipped N/Q/H residues before XYZ refinement:
A 421 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.121914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.094606 restraints weight = 8131.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 1.28
r_work: 0.2864 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2752 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2696
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2696 r_free = 0.2696    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2696 r_free = 0.2696    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2696
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8718
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7680  Z= 0.111
  Angle     :  0.508   5.287  10424  Z= 0.265
  Chirality :  0.038   0.124   1228
  Planarity :  0.004   0.039   1202
  Dihedral  : 12.629 118.781   1620
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.73 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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:  2.37 (0.29), residues: 876
  helix:  2.36 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.69 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 499 
 HIS   0.002   0.000   HIS A 200 
 PHE   0.013   0.001   PHE B 196 
 TYR   0.014   0.002   TYR A 195 
 ARG   0.011   0.001   ARG B 528 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03849 (  486)
  hydrogen bonds       : angle       3.54724 ( 1389)
  SS BOND              : bond        0.01184 (    2)
  SS BOND              : angle       2.83618 (    4)
  covalent geometry    : bond        0.00244 ( 7678)
  covalent geometry    : angle       0.50501 (10420)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.801 
Fit side-chains
REVERT: A   32 ARG cc_start: 0.7355 (mpt-90) cc_final: 0.6510 (mtp85)
REVERT: A   61 PHE cc_start: 0.7560 (m-10) cc_final: 0.6979 (m-80)
REVERT: A   68 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6973 (mm-30)
REVERT: A   70 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.7112 (ptp90)
REVERT: A  185 ARG cc_start: 0.7792 (ttp-170) cc_final: 0.6990 (ttm-80)
REVERT: A  304 GLU cc_start: 0.7193 (pm20) cc_final: 0.6786 (mp0)
REVERT: A  414 LYS cc_start: 0.5959 (OUTLIER) cc_final: 0.5628 (tppp)
REVERT: A  478 ARG cc_start: 0.8122 (mtp180) cc_final: 0.7863 (mtm180)
REVERT: A  529 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9035 (mp)
REVERT: B   65 SER cc_start: 0.7767 (OUTLIER) cc_final: 0.7563 (p)
REVERT: B  185 ARG cc_start: 0.7772 (ttp-170) cc_final: 0.7056 (ttm-80)
REVERT: B  295 GLU cc_start: 0.8097 (mp0) cc_final: 0.7821 (mp0)
REVERT: B  529 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9034 (mp)
  outliers start: 15
  outliers final: 8
  residues processed: 108
  average time/residue: 1.2211
  time to fit residues: 139.7002
Evaluate side-chains
  110 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue   70 ARG
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  414 LYS
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  301 LYS
Chi-restraints excluded: chain B residue  529 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0980
   chunk 11 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 32 optimal weight:    0.4980
   chunk 63 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 421 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.121617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.094321 restraints weight = 8058.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 1.29
r_work: 0.2820 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2704 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2692
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2692 r_free = 0.2692    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2692 r_free = 0.2692    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2692
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7680  Z= 0.109
  Angle     :  0.504   5.285  10424  Z= 0.263
  Chirality :  0.038   0.123   1228
  Planarity :  0.004   0.038   1202
  Dihedral  : 12.574 119.224   1620
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.98 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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:  2.41 (0.29), residues: 876
  helix:  2.40 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.70 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 285 
 HIS   0.002   0.000   HIS A 200 
 PHE   0.013   0.001   PHE B 196 
 TYR   0.014   0.002   TYR B 195 
 ARG   0.010   0.001   ARG B 528 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03796 (  486)
  hydrogen bonds       : angle       3.53317 ( 1389)
  SS BOND              : bond        0.01155 (    2)
  SS BOND              : angle       2.85047 (    4)
  covalent geometry    : bond        0.00239 ( 7678)
  covalent geometry    : angle       0.50062 (10420)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.839 
Fit side-chains
REVERT: A   32 ARG cc_start: 0.7319 (mpt-90) cc_final: 0.6456 (mtp85)
REVERT: A   61 PHE cc_start: 0.7512 (m-10) cc_final: 0.6927 (m-80)
REVERT: A   68 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6945 (mm-30)
REVERT: A   70 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.7072 (ptp90)
REVERT: A  185 ARG cc_start: 0.7752 (ttp-170) cc_final: 0.6933 (ttm-80)
REVERT: A  304 GLU cc_start: 0.7151 (pm20) cc_final: 0.6757 (mp0)
REVERT: A  414 LYS cc_start: 0.5928 (OUTLIER) cc_final: 0.5601 (tppp)
REVERT: A  478 ARG cc_start: 0.8092 (mtp180) cc_final: 0.7633 (mtm180)
REVERT: A  529 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9009 (mp)
REVERT: B   65 SER cc_start: 0.7727 (OUTLIER) cc_final: 0.7503 (p)
REVERT: B  185 ARG cc_start: 0.7723 (ttp-170) cc_final: 0.6995 (ttm-80)
REVERT: B  295 GLU cc_start: 0.8094 (mp0) cc_final: 0.7819 (mp0)
REVERT: B  529 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9009 (mp)
  outliers start: 14
  outliers final: 8
  residues processed: 106
  average time/residue: 1.3119
  time to fit residues: 147.2000
Evaluate side-chains
  111 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 VAL
Chi-restraints excluded: chain A residue   68 GLU
Chi-restraints excluded: chain A residue   70 ARG
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  414 LYS
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  301 LYS
Chi-restraints excluded: chain B residue  529 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 78 optimal weight:    0.5980
   chunk 81 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0370
   overall best weight:    0.5458

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.122828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.095795 restraints weight = 8209.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 1.28
r_work: 0.2835 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2747
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2747
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8707
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7680  Z= 0.103
  Angle     :  0.492   5.268  10424  Z= 0.257
  Chirality :  0.037   0.121   1228
  Planarity :  0.004   0.038   1202
  Dihedral  : 12.474 120.325   1620
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.73 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    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:  2.49 (0.29), residues: 876
  helix:  2.46 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.68 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 499 
 HIS   0.001   0.000   HIS A 200 
 PHE   0.013   0.001   PHE B 196 
 TYR   0.014   0.002   TYR B 195 
 ARG   0.010   0.001   ARG B 528 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03644 (  486)
  hydrogen bonds       : angle       3.49636 ( 1389)
  SS BOND              : bond        0.01127 (    2)
  SS BOND              : angle       2.76509 (    4)
  covalent geometry    : bond        0.00224 ( 7678)
  covalent geometry    : angle       0.48934 (10420)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6822.68 seconds
wall clock time: 118 minutes 22.95 seconds (7102.95 seconds total)