Starting phenix.real_space_refine
on Fri Aug 22 20:12:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k66_36918/08_2025/8k66_36918.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k66_36918/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k66_36918/08_2025/8k66_36918.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k66_36918/08_2025/8k66_36918.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k66_36918/08_2025/8k66_36918.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k66_36918/08_2025/8k66_36918.map"
  }
  resolution = 2.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.93, per 1000 atoms: 0.38
  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: 0.55
  Conformation dependent library (CDL) restraints added in 431.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.24
  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: 1.07

  Time building geometry restraints manager: 0.68 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: 0.01
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:             6.720
  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:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.550
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.800
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.005   0.001   ARG A 294 
 TYR   0.015   0.002   TYR B 195 
 PHE   0.013   0.001   PHE B 196 
 TRP   0.006   0.001   TRP A 285 
 HIS   0.002   0.001   HIS B 200 

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

*********************** 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  : 0.286 
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: 0.7481 (mmpt)
REVERT: A  185 ARG cc_start: 0.7666 (ttp-170) cc_final: 0.7233 (ttm-80)
REVERT: A  304 GLU cc_start: 0.7311 (pm20) cc_final: 0.6993 (mp0)
REVERT: A  414 LYS cc_start: 0.6306 (OUTLIER) cc_final: 0.6037 (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: 0.6014
  time to fit residues: 88.9069
Evaluate side-chains
  114 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3343 r_free = 0.3343 target = 0.123270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.095099 restraints weight = 9881.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 1.36
r_work: 0.2798 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2669
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2669 r_free = 0.2669    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 = 0.2669 r_free = 0.2669    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2669
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7680  Z= 0.131
  Angle     :  0.551   6.492  10424  Z= 0.284
  Chirality :  0.039   0.126   1228
  Planarity :  0.004   0.041   1202
  Dihedral  : 14.880 158.107   1641
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 14.96 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.28), residues: 876
  helix:  1.68 (0.20), residues: 632
  sheet:  None (None), residues: 0
  loop : -1.05 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 528 
 TYR   0.015   0.002   TYR B 195 
 PHE   0.012   0.001   PHE B 196 
 TRP   0.006   0.001   TRP A 285 
 HIS   0.003   0.001   HIS A 483 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7678)
  covalent geometry    : angle       0.54867 (10420)
  SS BOND              : bond        0.01372 (    2)
  SS BOND              : angle       2.84607 (    4)
  hydrogen bonds       : bond        0.04532 (  486)
  hydrogen bonds       : angle       3.81725 ( 1389)

*********************** 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  : 0.296 
Fit side-chains
REVERT: A   61 PHE cc_start: 0.7714 (m-10) cc_final: 0.7278 (m-80)
REVERT: A   68 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6960 (mm-30)
REVERT: A  185 ARG cc_start: 0.7807 (ttp-170) cc_final: 0.6960 (ttm-80)
REVERT: A  213 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7277 (mmt180)
REVERT: A  304 GLU cc_start: 0.7111 (pm20) cc_final: 0.6764 (mp0)
REVERT: A  422 LEU cc_start: 0.8279 (tp) cc_final: 0.8068 (tp)
REVERT: A  529 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9015 (mp)
REVERT: B   70 ARG cc_start: 0.7153 (mtm-85) cc_final: 0.6944 (mpp80)
REVERT: B  185 ARG cc_start: 0.7760 (ttp-170) cc_final: 0.7029 (ttm-80)
REVERT: B  422 LEU cc_start: 0.8295 (tp) cc_final: 0.8073 (tp)
REVERT: B  529 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9026 (mp)
  outliers start: 21
  outliers final: 13
  residues processed: 120
  average time/residue: 0.5730
  time to fit residues: 72.5044
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  : 0.271 
-------------------------------------------------------------------------------
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 77 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 75 optimal weight:    0.1980
   chunk 59 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   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 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 = 0.3379 r_free = 0.3379 target = 0.125429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.096779 restraints weight = 11982.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 1.50
r_work: 0.2791 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2672 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2747
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.079         |
| 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) = 0.079         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2747
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8740
moved from start:          0.1366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7680  Z= 0.115
  Angle     :  0.512   5.937  10424  Z= 0.266
  Chirality :  0.038   0.123   1228
  Planarity :  0.004   0.041   1202
  Dihedral  : 13.846 156.056   1626
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.22 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.29), residues: 876
  helix:  2.11 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.81 (0.40), residues: 238

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 7678)
  covalent geometry    : angle       0.50926 (10420)
  SS BOND              : bond        0.01264 (    2)
  SS BOND              : angle       2.74794 (    4)
  hydrogen bonds       : bond        0.04034 (  486)
  hydrogen bonds       : angle       3.65114 ( 1389)

*********************** 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
  126 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A   61 PHE cc_start: 0.7679 (m-10) cc_final: 0.7182 (m-80)
REVERT: A   68 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6974 (mm-30)
REVERT: A   70 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.7088 (ptp90)
REVERT: A  185 ARG cc_start: 0.7835 (ttp-170) cc_final: 0.6961 (ttm-80)
REVERT: A  304 GLU cc_start: 0.7094 (pm20) cc_final: 0.6757 (mp0)
REVERT: A  422 LEU cc_start: 0.8288 (tp) cc_final: 0.8071 (tp)
REVERT: A  478 ARG cc_start: 0.8136 (mtp180) cc_final: 0.7720 (mtm180)
REVERT: A  529 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9021 (mp)
REVERT: B   70 ARG cc_start: 0.7177 (mtm-85) cc_final: 0.6784 (mpp-170)
REVERT: B  185 ARG cc_start: 0.7787 (ttp-170) cc_final: 0.7044 (ttm-80)
REVERT: B  422 LEU cc_start: 0.8291 (tp) cc_final: 0.8070 (tp)
REVERT: B  529 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9067 (mp)
  outliers start: 18
  outliers final: 7
  residues processed: 118
  average time/residue: 0.5867
  time to fit residues: 72.8176
Evaluate side-chains
  114 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
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 67 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 74 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3303 r_free = 0.3303 target = 0.120430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.092840 restraints weight = 8479.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.2921 rms_B_bonded: 1.31
r_work: 0.2808 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2692 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2664
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2664 r_free = 0.2664    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 = 0.2664 r_free = 0.2664    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2664
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8741
moved from start:          0.1377

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= 0.132
  Angle     :  0.537   5.335  10424  Z= 0.280
  Chirality :  0.039   0.130   1228
  Planarity :  0.004   0.040   1202
  Dihedral  : 13.512 149.341   1620
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 15.47 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.08 (0.29), residues: 876
  helix:  2.14 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.76 (0.40), residues: 238

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 7678)
  covalent geometry    : angle       0.53420 (10420)
  SS BOND              : bond        0.01305 (    2)
  SS BOND              : angle       3.01677 (    4)
  hydrogen bonds       : bond        0.04364 (  486)
  hydrogen bonds       : angle       3.64123 ( 1389)

*********************** 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
  123 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A   61 PHE cc_start: 0.7635 (m-10) cc_final: 0.7140 (m-80)
REVERT: A   68 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6979 (mm-30)
REVERT: A   70 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7135 (ptp90)
REVERT: A  185 ARG cc_start: 0.7813 (ttp-170) cc_final: 0.6949 (ttm-80)
REVERT: A  304 GLU cc_start: 0.7119 (pm20) cc_final: 0.6733 (mp0)
REVERT: A  422 LEU cc_start: 0.8280 (tp) cc_final: 0.8065 (tp)
REVERT: A  478 ARG cc_start: 0.8132 (mtp180) cc_final: 0.7682 (mtm180)
REVERT: A  529 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9024 (mp)
REVERT: B   70 ARG cc_start: 0.7205 (mtm-85) cc_final: 0.6810 (mpp-170)
REVERT: B  185 ARG cc_start: 0.7764 (ttp-170) cc_final: 0.7054 (ttm-80)
REVERT: B  422 LEU cc_start: 0.8302 (tp) cc_final: 0.8084 (tp)
REVERT: B  486 SER cc_start: 0.7505 (OUTLIER) cc_final: 0.7079 (p)
REVERT: B  529 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9068 (mp)
  outliers start: 17
  outliers final: 8
  residues processed: 116
  average time/residue: 0.5714
  time to fit residues: 69.7718
Evaluate side-chains
  114 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
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  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 9 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 77 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0670
   chunk 25 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.5918

-------------------------------------------------------------------------------
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 = 0.3331 r_free = 0.3331 target = 0.122569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.094712 restraints weight = 9056.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 1.35
r_work: 0.2830 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2712 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2698
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2698 r_free = 0.2698    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 = 0.2698 r_free = 0.2698    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2698
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
moved from start:          0.1570

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= 0.107
  Angle     :  0.494   5.279  10424  Z= 0.258
  Chirality :  0.037   0.123   1228
  Planarity :  0.004   0.039   1202
  Dihedral  : 13.052 146.693   1620
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.35 (0.29), residues: 876
  helix:  2.34 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.67 (0.40), residues: 238

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 7678)
  covalent geometry    : angle       0.49084 (10420)
  SS BOND              : bond        0.01235 (    2)
  SS BOND              : angle       2.78861 (    4)
  hydrogen bonds       : bond        0.03730 (  486)
  hydrogen bonds       : angle       3.54152 ( 1389)

*********************** 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
  120 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A   61 PHE cc_start: 0.7558 (m-10) cc_final: 0.6997 (m-80)
REVERT: A   68 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6984 (mm-30)
REVERT: A   70 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.7088 (ptp90)
REVERT: A  185 ARG cc_start: 0.7799 (ttp-170) cc_final: 0.6933 (ttm-80)
REVERT: A  304 GLU cc_start: 0.7114 (pm20) cc_final: 0.6740 (mp0)
REVERT: A  478 ARG cc_start: 0.8098 (mtp180) cc_final: 0.7654 (mtm180)
REVERT: A  486 SER cc_start: 0.7644 (OUTLIER) cc_final: 0.7251 (p)
REVERT: A  529 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9039 (mp)
REVERT: B   70 ARG cc_start: 0.7197 (mtm-85) cc_final: 0.6803 (mpp-170)
REVERT: B  185 ARG cc_start: 0.7758 (ttp-170) cc_final: 0.7034 (ttm-80)
REVERT: B  304 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6758 (pm20)
REVERT: B  529 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9032 (mp)
  outliers start: 14
  outliers final: 7
  residues processed: 115
  average time/residue: 0.5867
  time to fit residues: 70.9898
Evaluate side-chains
  110 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
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  529 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0470
   chunk 83 optimal weight:    0.4980
   chunk 0 optimal weight:    7.9990
   chunk 28 optimal weight:    0.5980
   chunk 75 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 77 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.5078

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.122706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.093961 restraints weight = 10924.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 1.49
r_work: 0.2842 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2725 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2693
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2693 r_free = 0.2693    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 = 0.2693 r_free = 0.2693    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2693
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8705
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7680  Z= 0.101
  Angle     :  0.486   5.553  10424  Z= 0.254
  Chirality :  0.037   0.118   1228
  Planarity :  0.004   0.039   1202
  Dihedral  : 12.566 140.858   1620
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.86 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.50 (0.29), residues: 876
  helix:  2.46 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.65 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 528 
 TYR   0.014   0.002   TYR B 195 
 PHE   0.013   0.001   PHE B 196 
 TRP   0.006   0.001   TRP A 285 
 HIS   0.001   0.000   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 7678)
  covalent geometry    : angle       0.48288 (10420)
  SS BOND              : bond        0.01198 (    2)
  SS BOND              : angle       2.74884 (    4)
  hydrogen bonds       : bond        0.03566 (  486)
  hydrogen bonds       : angle       3.49265 ( 1389)

*********************** 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
  120 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A   32 ARG cc_start: 0.7368 (mpt-90) cc_final: 0.6506 (mtp85)
REVERT: A   68 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6946 (mm-30)
REVERT: A   70 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.7069 (ptp90)
REVERT: A  185 ARG cc_start: 0.7821 (ttp-170) cc_final: 0.6943 (ttm-80)
REVERT: A  304 GLU cc_start: 0.7141 (pm20) cc_final: 0.6764 (mp0)
REVERT: A  478 ARG cc_start: 0.8120 (mtp180) cc_final: 0.7657 (mtm180)
REVERT: A  486 SER cc_start: 0.7591 (OUTLIER) cc_final: 0.7277 (p)
REVERT: B   70 ARG cc_start: 0.7152 (mtm-85) cc_final: 0.6785 (mpp-170)
REVERT: B  185 ARG cc_start: 0.7777 (ttp-170) cc_final: 0.7054 (ttm-80)
REVERT: B  304 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6735 (pm20)
  outliers start: 14
  outliers final: 7
  residues processed: 113
  average time/residue: 0.5862
  time to fit residues: 69.7562
Evaluate side-chains
  107 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 67 optimal weight:    0.1980
   chunk 13 optimal weight:    1.9990
   chunk 28 optimal weight:    0.3980
   chunk 61 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 = 0.3322 r_free = 0.3322 target = 0.122046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.094273 restraints weight = 8398.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.2971 rms_B_bonded: 1.32
r_work: 0.2863 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2750 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2695
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2695 r_free = 0.2695    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 = 0.2695 r_free = 0.2695    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2695
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8709
moved from start:          0.1649

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= 0.109
  Angle     :  0.496   5.325  10424  Z= 0.259
  Chirality :  0.037   0.122   1228
  Planarity :  0.004   0.038   1202
  Dihedral  : 12.505 132.364   1620
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.86 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.47 (0.29), residues: 876
  helix:  2.44 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.63 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 528 
 TYR   0.015   0.002   TYR B 195 
 PHE   0.013   0.001   PHE B 196 
 TRP   0.004   0.001   TRP A  42 
 HIS   0.002   0.000   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 7678)
  covalent geometry    : angle       0.49281 (10420)
  SS BOND              : bond        0.01216 (    2)
  SS BOND              : angle       2.91402 (    4)
  hydrogen bonds       : bond        0.03817 (  486)
  hydrogen bonds       : angle       3.50704 ( 1389)

*********************** 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
  116 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A   32 ARG cc_start: 0.7386 (mpt-90) cc_final: 0.6522 (mtp85)
REVERT: A   68 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6921 (mm-30)
REVERT: A   70 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.7085 (ptp90)
REVERT: A  185 ARG cc_start: 0.7787 (ttp-170) cc_final: 0.6949 (ttm-80)
REVERT: A  304 GLU cc_start: 0.7175 (pm20) cc_final: 0.6778 (mp0)
REVERT: A  422 LEU cc_start: 0.8297 (tp) cc_final: 0.8094 (tp)
REVERT: A  478 ARG cc_start: 0.8101 (mtp180) cc_final: 0.7825 (mtm180)
REVERT: A  486 SER cc_start: 0.7639 (OUTLIER) cc_final: 0.7296 (p)
REVERT: B   70 ARG cc_start: 0.7110 (mtm-85) cc_final: 0.6736 (mpp-170)
REVERT: B  185 ARG cc_start: 0.7770 (ttp-170) cc_final: 0.7040 (ttm-80)
REVERT: B  295 GLU cc_start: 0.8043 (mp0) cc_final: 0.7749 (mp0)
REVERT: B  304 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6775 (pm20)
  outliers start: 12
  outliers final: 7
  residues processed: 112
  average time/residue: 0.5666
  time to fit residues: 66.9356
Evaluate side-chains
  110 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 50 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3316 r_free = 0.3316 target = 0.121375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.094081 restraints weight = 8095.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 1.28
r_work: 0.2836 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2721 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2693
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2693 r_free = 0.2693    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 = 0.2693 r_free = 0.2693    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2693
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8725
moved from start:          0.1612

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= 0.120
  Angle     :  0.515   5.350  10424  Z= 0.268
  Chirality :  0.038   0.152   1228
  Planarity :  0.004   0.039   1202
  Dihedral  : 12.530 121.971   1620
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.98 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.29), residues: 876
  helix:  2.38 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.70 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 528 
 TYR   0.015   0.002   TYR A 195 
 PHE   0.013   0.001   PHE B 196 
 TRP   0.005   0.001   TRP B 499 
 HIS   0.002   0.000   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 7678)
  covalent geometry    : angle       0.51176 (10420)
  SS BOND              : bond        0.01221 (    2)
  SS BOND              : angle       3.01137 (    4)
  hydrogen bonds       : bond        0.04054 (  486)
  hydrogen bonds       : angle       3.54015 ( 1389)

*********************** 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
  115 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A   68 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6938 (mm-30)
REVERT: A   70 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7156 (ptp90)
REVERT: A  185 ARG cc_start: 0.7783 (ttp-170) cc_final: 0.6949 (ttm-80)
REVERT: A  304 GLU cc_start: 0.7196 (pm20) cc_final: 0.6801 (mp0)
REVERT: A  478 ARG cc_start: 0.8123 (mtp180) cc_final: 0.7843 (mtm180)
REVERT: A  486 SER cc_start: 0.7674 (OUTLIER) cc_final: 0.7268 (p)
REVERT: B   70 ARG cc_start: 0.7131 (mtm-85) cc_final: 0.6758 (mpp-170)
REVERT: B  185 ARG cc_start: 0.7770 (ttp-170) cc_final: 0.7041 (ttm-80)
REVERT: B  295 GLU cc_start: 0.8078 (mp0) cc_final: 0.7697 (mp0)
  outliers start: 12
  outliers final: 9
  residues processed: 110
  average time/residue: 0.5743
  time to fit residues: 66.6124
Evaluate side-chains
  115 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
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  300 ILE
Chi-restraints excluded: chain A residue  486 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  304 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3308 r_free = 0.3308 target = 0.120764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.093657 restraints weight = 7877.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.2927 rms_B_bonded: 1.26
r_work: 0.2815 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2700 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2679
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2679 r_free = 0.2679    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2679 r_free = 0.2679    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2679
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8729
moved from start:          0.1580

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= 0.129
  Angle     :  0.530   5.364  10424  Z= 0.275
  Chirality :  0.039   0.148   1228
  Planarity :  0.004   0.039   1202
  Dihedral  : 12.624 117.362   1620
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 16.50 %
    Favored  : 81.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.24 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.30 (0.29), residues: 876
  helix:  2.32 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.72 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 528 
 TYR   0.016   0.002   TYR A 195 
 PHE   0.013   0.001   PHE B 196 
 TRP   0.006   0.001   TRP B 499 
 HIS   0.002   0.000   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7678)
  covalent geometry    : angle       0.52701 (10420)
  SS BOND              : bond        0.01216 (    2)
  SS BOND              : angle       3.07121 (    4)
  hydrogen bonds       : bond        0.04218 (  486)
  hydrogen bonds       : angle       3.56778 ( 1389)

*********************** 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
  117 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A   32 ARG cc_start: 0.7360 (mpt-90) cc_final: 0.6499 (mtp85)
REVERT: A   61 PHE cc_start: 0.7577 (m-10) cc_final: 0.7011 (m-80)
REVERT: A   68 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6934 (mm-30)
REVERT: A   70 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7149 (ptp90)
REVERT: A  185 ARG cc_start: 0.7786 (ttp-170) cc_final: 0.6948 (ttm-80)
REVERT: A  304 GLU cc_start: 0.7186 (pm20) cc_final: 0.6785 (mp0)
REVERT: A  478 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7843 (mtm180)
REVERT: A  486 SER cc_start: 0.7680 (OUTLIER) cc_final: 0.7463 (t)
REVERT: B   70 ARG cc_start: 0.7133 (mtm-85) cc_final: 0.6753 (mpp-170)
REVERT: B  185 ARG cc_start: 0.7768 (ttp-170) cc_final: 0.7035 (ttm-80)
REVERT: B  295 GLU cc_start: 0.8102 (mp0) cc_final: 0.7896 (mp0)
  outliers start: 12
  outliers final: 7
  residues processed: 112
  average time/residue: 0.5710
  time to fit residues: 67.3077
Evaluate side-chains
  113 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
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 B residue   84 LEU
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  300 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 80 optimal weight:    0.1980
   chunk 71 optimal weight:    0.9980
   chunk 78 optimal weight:    0.1980
   chunk 39 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 22 optimal weight:    0.3980
   chunk 23 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0870
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.2958

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.124452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.096608 restraints weight = 9070.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 1.37
r_work: 0.2850 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2734 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2732
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2732 r_free = 0.2732    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2732 r_free = 0.2732    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2732
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7680  Z= 0.089
  Angle     :  0.466   5.269  10424  Z= 0.243
  Chirality :  0.037   0.136   1228
  Planarity :  0.004   0.036   1202
  Dihedral  : 12.310 122.585   1620
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 17.26 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.66 (0.29), residues: 876
  helix:  2.62 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.71 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 528 
 TYR   0.013   0.001   TYR B 195 
 PHE   0.012   0.001   PHE B 196 
 TRP   0.007   0.001   TRP A 285 
 HIS   0.001   0.000   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00184 ( 7678)
  covalent geometry    : angle       0.46366 (10420)
  SS BOND              : bond        0.01084 (    2)
  SS BOND              : angle       2.66275 (    4)
  hydrogen bonds       : bond        0.03228 (  486)
  hydrogen bonds       : angle       3.46917 ( 1389)

********************** 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
  109 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A   32 ARG cc_start: 0.7310 (mpt-90) cc_final: 0.6438 (mtp85)
REVERT: A   68 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6919 (mm-30)
REVERT: A  185 ARG cc_start: 0.7746 (ttp-170) cc_final: 0.6874 (ttm-80)
REVERT: A  304 GLU cc_start: 0.7140 (pm20) cc_final: 0.6670 (mp0)
REVERT: A  478 ARG cc_start: 0.8058 (mtp180) cc_final: 0.7714 (mtm180)
REVERT: B   70 ARG cc_start: 0.7104 (mtm-85) cc_final: 0.6734 (mpp-170)
REVERT: B  185 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.7006 (ttm-80)
REVERT: B  295 GLU cc_start: 0.8110 (mp0) cc_final: 0.7711 (mp0)
  outliers start: 8
  outliers final: 6
  residues processed: 105
  average time/residue: 0.5991
  time to fit residues: 66.3080
Evaluate side-chains
  107 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
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   84 LEU
Chi-restraints excluded: chain A residue  107 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 62 optimal weight:    0.7980
   chunk 42 optimal weight:    0.2980
   chunk 10 optimal weight:    4.9990
   chunk 35 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3347 r_free = 0.3347 target = 0.123409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.097035 restraints weight = 8530.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.2954 rms_B_bonded: 1.26
r_work: 0.2846 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2734 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2740
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2740 r_free = 0.2740    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2740 r_free = 0.2740    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2740
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8727
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7680  Z= 0.116
  Angle     :  0.513   5.339  10424  Z= 0.266
  Chirality :  0.038   0.142   1228
  Planarity :  0.004   0.038   1202
  Dihedral  : 12.384 120.566   1620
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 17.39 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.50 (0.29), residues: 876
  helix:  2.47 (0.20), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.67 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 528 
 TYR   0.016   0.002   TYR A 195 
 PHE   0.013   0.001   PHE B 196 
 TRP   0.006   0.001   TRP B 499 
 HIS   0.002   0.000   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7678)
  covalent geometry    : angle       0.50966 (10420)
  SS BOND              : bond        0.01161 (    2)
  SS BOND              : angle       2.88481 (    4)
  hydrogen bonds       : bond        0.03957 (  486)
  hydrogen bonds       : angle       3.51589 ( 1389)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3213.49 seconds
wall clock time: 55 minutes 20.26 seconds (3320.26 seconds total)