Starting phenix.real_space_refine
on Thu Sep 18 01:34:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dvj_47208/09_2025/9dvj_47208_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dvj_47208/09_2025/9dvj_47208.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dvj_47208/09_2025/9dvj_47208_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dvj_47208/09_2025/9dvj_47208_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dvj_47208/09_2025/9dvj_47208.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dvj_47208/09_2025/9dvj_47208.map"
  }
  resolution = 2.52
  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=   0.023
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       4      5.49       5
     S      32      5.16       5
     C    4370      2.51       5
     N    1004      2.21       5
     O    1042      1.98       5
     H    6258      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12710
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6270
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 6270
          Classifications: {'peptide': 377}
          Link IDs: {'PTRANS': 13, 'TRANS': 363}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 6270
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 6270
          Classifications: {'peptide': 377}
          Link IDs: {'PTRANS': 13, 'TRANS': 363}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 85
          Unusual residues: {'CLR': 1, 'CPL': 1, 'PO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 85
          Unusual residues: {'CLR': 1, 'CPL': 1, 'PO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.78, per 1000 atoms: 0.22
  Number of scatterers: 12710
  At special positions: 0
  Unit cell: (75.946, 78.4225, 127.127, 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      32     16.00
     P       4     15.00
     O    1042      8.00
     N    1004      7.00
     C    4370      6.00
     H    6258      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 440 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 440 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Conformation dependent library (CDL) restraints added in 360.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1432

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 0 sheets defined
      81.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 230 through 257
    Processing helix  chain 'A' and resid 267 through 296
      removed outlier: 4.327A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
    Processing helix  chain 'A' and resid 312 through 337
    Processing helix  chain 'A' and resid 345 through 360
    Processing helix  chain 'A' and resid 367 through 383
    Processing helix  chain 'A' and resid 390 through 403
    Processing helix  chain 'A' and resid 403 through 419
      removed outlier: 4.089A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 445 through 453
    Processing helix  chain 'A' and resid 453 through 471
    Processing helix  chain 'A' and resid 472 through 502
      removed outlier: 4.097A  pdb=" N   HIS A 476 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL A 478 " --> pdb=" O   PHE A 474 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   ASN A 479 " --> pdb=" O   PRO A 475 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 532
    Processing helix  chain 'A' and resid 555 through 582
      removed outlier: 4.027A  pdb=" N   TYR A 559 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   PHE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 618
      Proline residue:  A 598  - end of helix
    Processing helix  chain 'B' and resid 230 through 257
    Processing helix  chain 'B' and resid 267 through 296
      removed outlier: 4.211A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 304
    Processing helix  chain 'B' and resid 312 through 337
    Processing helix  chain 'B' and resid 345 through 360
    Processing helix  chain 'B' and resid 367 through 383
    Processing helix  chain 'B' and resid 390 through 403
    Processing helix  chain 'B' and resid 403 through 419
      removed outlier: 4.038A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 443
    Processing helix  chain 'B' and resid 445 through 471
      removed outlier: 3.545A  pdb=" N   ALA B 449 " --> pdb=" O   TYR B 445 " (cutoff:3.500A)
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'B' and resid 472 through 502
      removed outlier: 3.955A  pdb=" N   HIS B 476 " --> pdb=" O   ARG B 472 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL B 478 " --> pdb=" O   PHE B 474 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ASN B 479 " --> pdb=" O   PRO B 475 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 532
    Processing helix  chain 'B' and resid 555 through 582
      removed outlier: 3.951A  pdb=" N   TYR B 559 " --> pdb=" O   GLN B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 618
      removed outlier: 4.640A  pdb=" N   ASP B 590 " --> pdb=" O   PRO B 586 " (cutoff:3.500A)
      removed outlier: 5.168A  pdb=" N   ILE B 591 " --> pdb=" O   HIS B 587 " (cutoff:3.500A)
      Proline residue:  B 598  - end of helix

    466 hydrogen bonds defined for protein.
    1398 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.91

  Time building geometry restraints manager: 1.40 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6242
        1.03 -     1.23: 23
        1.23 -     1.42: 2945
        1.42 -     1.62: 3666
        1.62 -     1.81: 48
  Bond restraints: 12924
  Sorted by residual:
  bond pdb=" O3P CPL B 803 "
       pdb=" P   CPL B 803 "
    ideal  model  delta    sigma   weight residual
    1.633  1.740 -0.107 2.00e-02 2.50e+03 2.87e+01
  bond pdb=" O3P CPL A 803 "
       pdb=" P   CPL A 803 "
    ideal  model  delta    sigma   weight residual
    1.633  1.740 -0.107 2.00e-02 2.50e+03 2.86e+01
  bond pdb=" O4P CPL A 803 "
       pdb=" P   CPL A 803 "
    ideal  model  delta    sigma   weight residual
    1.648  1.714 -0.066 2.00e-02 2.50e+03 1.09e+01
  bond pdb=" O4P CPL B 803 "
       pdb=" P   CPL B 803 "
    ideal  model  delta    sigma   weight residual
    1.648  1.713 -0.065 2.00e-02 2.50e+03 1.06e+01
  bond pdb=" N   TRP B 534 "
       pdb=" H   TRP B 534 "
    ideal  model  delta    sigma   weight residual
    0.860  0.914 -0.054 2.00e-02 2.50e+03 7.18e+00
  ... (remaining 12919 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.05: 23083
        3.05 -     6.10: 64
        6.10 -     9.14: 9
        9.14 -    12.19: 2
       12.19 -    15.24: 2
  Bond angle restraints: 23160
  Sorted by residual:
  angle pdb=" O1P CPL A 803 "
        pdb=" P   CPL A 803 "
        pdb=" O2P CPL A 803 "
      ideal   model   delta    sigma   weight residual
     119.55  134.79  -15.24 3.00e+00 1.11e-01 2.58e+01
  angle pdb=" O1P CPL B 803 "
        pdb=" P   CPL B 803 "
        pdb=" O2P CPL B 803 "
      ideal   model   delta    sigma   weight residual
     119.55  134.72  -15.17 3.00e+00 1.11e-01 2.56e+01
  angle pdb=" CA  PHE B 366 "
        pdb=" C   PHE B 366 "
        pdb=" O   PHE B 366 "
      ideal   model   delta    sigma   weight residual
     120.85  115.50    5.35 1.67e+00 3.59e-01 1.03e+01
  angle pdb=" N   CPL B 803 "
        pdb=" C5  CPL B 803 "
        pdb=" C4  CPL B 803 "
      ideal   model   delta    sigma   weight residual
     117.50  108.06    9.44 3.00e+00 1.11e-01 9.90e+00
  angle pdb=" N   CPL A 803 "
        pdb=" C5  CPL A 803 "
        pdb=" C4  CPL A 803 "
      ideal   model   delta    sigma   weight residual
     117.50  108.12    9.38 3.00e+00 1.11e-01 9.77e+00
  ... (remaining 23155 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.48: 5932
       27.48 -    54.96: 281
       54.96 -    82.44: 38
       82.44 -   109.92: 2
      109.92 -   137.40: 5
  Dihedral angle restraints: 6258
    sinusoidal: 3264
      harmonic: 2994
  Sorted by residual:
  dihedral pdb=" C3  CPL A 803 "
           pdb=" C1  CPL A 803 "
           pdb=" C2  CPL A 803 "
           pdb=" O3P CPL A 803 "
      ideal   model   delta sinusoidal    sigma   weight residual
      72.09  -65.31  137.40     1      3.00e+01 1.11e-03 1.85e+01
  dihedral pdb=" O2  CPL A 803 "
           pdb=" C1  CPL A 803 "
           pdb=" C2  CPL A 803 "
           pdb=" O3P CPL A 803 "
      ideal   model   delta sinusoidal    sigma   weight residual
     309.18  174.01  135.17     1      3.00e+01 1.11e-03 1.82e+01
  dihedral pdb=" C33 CPL B 803 "
           pdb=" C31 CPL B 803 "
           pdb=" C32 CPL B 803 "
           pdb=" O2  CPL B 803 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.65   47.74  123.91     1      3.00e+01 1.11e-03 1.66e+01
  ... (remaining 6255 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 898
       0.073 -    0.147: 77
       0.147 -    0.220: 1
       0.220 -    0.293: 2
       0.293 -    0.367: 8
  Chirality restraints: 986
  Sorted by residual:
  chirality pdb=" C17 CLR A 802 "
            pdb=" C13 CLR A 802 "
            pdb=" C16 CLR A 802 "
            pdb=" C20 CLR A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.92   -0.37 2.00e-01 2.50e+01 3.36e+00
  chirality pdb=" C17 CLR B 802 "
            pdb=" C13 CLR B 802 "
            pdb=" C16 CLR B 802 "
            pdb=" C20 CLR B 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.91   -0.36 2.00e-01 2.50e+01 3.22e+00
  chirality pdb=" C13 CLR A 802 "
            pdb=" C12 CLR A 802 "
            pdb=" C14 CLR A 802 "
            pdb=" C17 CLR A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -3.27    0.34 2.00e-01 2.50e+01 2.82e+00
  ... (remaining 983 not shown)

  Planarity restraints: 1802
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 366 "   -0.021 2.00e-02 2.50e+03   3.98e-02 1.58e+01
        pdb=" N   TYR B 367 "    0.068 2.00e-02 2.50e+03
        pdb=" CA  TYR B 367 "   -0.018 2.00e-02 2.50e+03
        pdb=" H   TYR B 367 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 366 "   -0.014 2.00e-02 2.50e+03   2.85e-02 8.15e+00
        pdb=" C   PHE B 366 "    0.049 2.00e-02 2.50e+03
        pdb=" O   PHE B 366 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   TYR B 367 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 534 "    0.010 2.00e-02 2.50e+03   1.95e-02 3.79e+00
        pdb=" C   TRP B 534 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   TRP B 534 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLY B 535 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1799 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.22: 921
        2.22 -     2.81: 26631
        2.81 -     3.41: 37281
        3.41 -     4.00: 47682
        4.00 -     4.60: 73473
  Nonbonded interactions: 185988
  Sorted by model distance:
  nonbonded pdb=" O   ILE B 271 "
            pdb=" HH  TYR B 352 "
     model   vdw
     1.620 2.450
  nonbonded pdb=" O   LYS B 482 "
            pdb=" HG1 THR B 485 "
     model   vdw
     1.629 2.450
  nonbonded pdb=" O   LYS A 482 "
            pdb=" HG1 THR A 485 "
     model   vdw
     1.647 2.450
  nonbonded pdb=" O   ILE A 271 "
            pdb=" HH  TYR A 352 "
     model   vdw
     1.649 2.450
  nonbonded pdb="HH12 ARG B 466 "
            pdb=" O   GLY B 621 "
     model   vdw
     1.657 2.450
  ... (remaining 185983 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'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.340
  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:             0.090
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.980
  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:7.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.107   6668  Z= 0.224
  Angle     :  0.651  15.241   9066  Z= 0.288
  Chirality :  0.048   0.367    986
  Planarity :  0.003   0.039   1080
  Dihedral  : 17.140 137.402   2442
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 15.62 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  3.78 (0.30), residues: 742
  helix:  3.53 (0.20), residues: 572
  sheet:  None (None), residues: 0
  loop : -1.47 (0.41), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 380 
 TYR   0.009   0.001   TYR A 496 
 PHE   0.013   0.001   PHE A 610 
 TRP   0.009   0.001   TRP B 327 
 HIS   0.002   0.000   HIS B 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 6666)
  covalent geometry    : angle       0.65066 ( 9062)
  SS BOND              : bond        0.00180 (    2)
  SS BOND              : angle       0.48527 (    4)
  hydrogen bonds       : bond        0.08683 (  466)
  hydrogen bonds       : angle       4.37064 ( 1398)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.7300 (m-80) cc_final: 0.7046 (m-10)
REVERT: A  366 PHE cc_start: 0.8448 (m-80) cc_final: 0.8246 (m-80)
REVERT: A  487 PHE cc_start: 0.6648 (m-10) cc_final: 0.5769 (m-80)
REVERT: A  539 LYS cc_start: 0.8010 (pttt) cc_final: 0.7335 (mmtm)
REVERT: A  550 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6943 (mt-10)
REVERT: B  550 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6925 (tt0)
  outliers start: 5
  outliers final: 3
  residues processed: 107
  average time/residue: 0.8584
  time to fit residues: 98.4904
Evaluate side-chains
  63 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  609 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0770
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.2980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
B 499 HIS
B 576 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.144165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.114869 restraints weight = 22788.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.35
r_work: 0.3429 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3306 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6668  Z= 0.140
  Angle     :  0.471   4.617   9066  Z= 0.254
  Chirality :  0.036   0.130    986
  Planarity :  0.004   0.039   1080
  Dihedral  : 12.251 116.902   1052
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 16.67 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  3.47 (0.30), residues: 742
  helix:  3.17 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -1.67 (0.44), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 293 
 TYR   0.011   0.001   TYR A 352 
 PHE   0.018   0.001   PHE A 605 
 TRP   0.011   0.001   TRP B 327 
 HIS   0.004   0.001   HIS B 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 6666)
  covalent geometry    : angle       0.47084 ( 9062)
  SS BOND              : bond        0.00305 (    2)
  SS BOND              : angle       1.09691 (    4)
  hydrogen bonds       : bond        0.04961 (  466)
  hydrogen bonds       : angle       4.14524 ( 1398)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.7349 (m-80) cc_final: 0.7002 (m-10)
REVERT: A  386 PHE cc_start: 0.8096 (m-10) cc_final: 0.7878 (m-10)
REVERT: A  539 LYS cc_start: 0.7973 (pttt) cc_final: 0.7208 (mmtm)
REVERT: A  550 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6942 (mt-10)
REVERT: B  411 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7688 (tm-30)
REVERT: B  472 ARG cc_start: 0.6702 (mtt180) cc_final: 0.6248 (mtp180)
REVERT: B  550 GLU cc_start: 0.7689 (mm-30) cc_final: 0.6987 (tt0)
  outliers start: 8
  outliers final: 2
  residues processed: 73
  average time/residue: 0.9498
  time to fit residues: 74.3866
Evaluate side-chains
  61 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  578 SER
Chi-restraints excluded: chain A residue  609 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 55 optimal weight:    0.3980
   chunk 70 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
B 310 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.132305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.102656 restraints weight = 23550.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 2.37
r_work: 0.3264 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3143 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6668  Z= 0.173
  Angle     :  0.511   6.680   9066  Z= 0.281
  Chirality :  0.037   0.126    986
  Planarity :  0.004   0.057   1080
  Dihedral  : 11.531 113.143   1048
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.17 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.88 (0.30), residues: 742
  helix:  2.75 (0.20), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.90 (0.44), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 293 
 TYR   0.014   0.002   TYR B 417 
 PHE   0.031   0.002   PHE A 605 
 TRP   0.015   0.002   TRP B 327 
 HIS   0.007   0.001   HIS B 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 6666)
  covalent geometry    : angle       0.51015 ( 9062)
  SS BOND              : bond        0.00435 (    2)
  SS BOND              : angle       1.17242 (    4)
  hydrogen bonds       : bond        0.06131 (  466)
  hydrogen bonds       : angle       4.22533 ( 1398)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.7445 (m-80) cc_final: 0.7027 (m-10)
REVERT: A  386 PHE cc_start: 0.8168 (m-10) cc_final: 0.7957 (m-10)
REVERT: A  472 ARG cc_start: 0.7458 (mtt-85) cc_final: 0.7058 (ttm-80)
REVERT: A  507 THR cc_start: 0.6596 (OUTLIER) cc_final: 0.6381 (m)
REVERT: A  550 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7186 (mt-10)
REVERT: B  306 ASN cc_start: 0.7037 (t0) cc_final: 0.6689 (t0)
REVERT: B  411 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7756 (tm-30)
REVERT: B  469 ASP cc_start: 0.7682 (m-30) cc_final: 0.7410 (m-30)
REVERT: B  472 ARG cc_start: 0.6971 (mtt180) cc_final: 0.6506 (mtp85)
REVERT: B  550 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7098 (tt0)
REVERT: B  613 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8588 (tm-30)
  outliers start: 15
  outliers final: 2
  residues processed: 82
  average time/residue: 0.9074
  time to fit residues: 79.3151
Evaluate side-chains
  62 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  507 THR
Chi-restraints excluded: chain B residue  401 ASN
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  613 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 608 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.130649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.101266 restraints weight = 23215.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 2.28
r_work: 0.3255 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6668  Z= 0.176
  Angle     :  0.490   5.524   9066  Z= 0.271
  Chirality :  0.037   0.165    986
  Planarity :  0.004   0.048   1080
  Dihedral  : 11.258 107.091   1046
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 15.92 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  2.75 (0.30), residues: 742
  helix:  2.66 (0.20), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.94 (0.44), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 570 
 TYR   0.011   0.001   TYR A 352 
 PHE   0.026   0.002   PHE A 605 
 TRP   0.011   0.001   TRP B 327 
 HIS   0.003   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 6666)
  covalent geometry    : angle       0.48881 ( 9062)
  SS BOND              : bond        0.00434 (    2)
  SS BOND              : angle       1.34923 (    4)
  hydrogen bonds       : bond        0.05960 (  466)
  hydrogen bonds       : angle       4.21853 ( 1398)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.7521 (m-80) cc_final: 0.7121 (m-10)
REVERT: A  472 ARG cc_start: 0.7460 (mtt-85) cc_final: 0.7108 (ttm-80)
REVERT: B  306 ASN cc_start: 0.7219 (t0) cc_final: 0.6850 (t0)
REVERT: B  411 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7663 (tm-30)
REVERT: B  472 ARG cc_start: 0.7058 (mtt180) cc_final: 0.6617 (mtp85)
REVERT: B  550 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7051 (tt0)
  outliers start: 11
  outliers final: 6
  residues processed: 68
  average time/residue: 1.0161
  time to fit residues: 73.3703
Evaluate side-chains
  59 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  498 THR
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  581 SER
Chi-restraints excluded: chain B residue  584 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 608 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.130325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.100205 restraints weight = 23202.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.34
r_work: 0.3233 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6668  Z= 0.168
  Angle     :  0.487   5.085   9066  Z= 0.270
  Chirality :  0.036   0.126    986
  Planarity :  0.004   0.051   1080
  Dihedral  : 10.899 100.136   1046
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.92 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.70 (0.30), residues: 742
  helix:  2.63 (0.20), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.96 (0.44), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 293 
 TYR   0.020   0.001   TYR B 368 
 PHE   0.026   0.001   PHE A 605 
 TRP   0.009   0.001   TRP B 327 
 HIS   0.004   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 6666)
  covalent geometry    : angle       0.48560 ( 9062)
  SS BOND              : bond        0.00509 (    2)
  SS BOND              : angle       1.51712 (    4)
  hydrogen bonds       : bond        0.05922 (  466)
  hydrogen bonds       : angle       4.19801 ( 1398)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.7448 (m-80) cc_final: 0.7059 (m-10)
REVERT: A  472 ARG cc_start: 0.7456 (mtt-85) cc_final: 0.7087 (ttm-80)
REVERT: B  306 ASN cc_start: 0.7266 (t0) cc_final: 0.7025 (t0)
REVERT: B  357 PHE cc_start: 0.6798 (m-10) cc_final: 0.5597 (t80)
REVERT: B  411 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7644 (tm-30)
REVERT: B  472 ARG cc_start: 0.7066 (mtt180) cc_final: 0.6607 (mtp85)
REVERT: B  550 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7093 (tt0)
  outliers start: 10
  outliers final: 7
  residues processed: 68
  average time/residue: 1.3171
  time to fit residues: 94.1947
Evaluate side-chains
  59 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  445 TYR
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain B residue  401 ASN
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  581 SER
Chi-restraints excluded: chain B residue  584 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 39 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.131110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.100831 restraints weight = 23153.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 2.34
r_work: 0.3241 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.3256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6668  Z= 0.148
  Angle     :  0.478   5.367   9066  Z= 0.264
  Chirality :  0.035   0.124    986
  Planarity :  0.004   0.039   1080
  Dihedral  : 10.658  96.628   1046
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 16.37 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  2.80 (0.30), residues: 742
  helix:  2.69 (0.20), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.89 (0.44), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 293 
 TYR   0.014   0.001   TYR B 368 
 PHE   0.023   0.001   PHE A 605 
 TRP   0.009   0.001   TRP A 514 
 HIS   0.022   0.001   HIS B 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6666)
  covalent geometry    : angle       0.47734 ( 9062)
  SS BOND              : bond        0.00446 (    2)
  SS BOND              : angle       1.42399 (    4)
  hydrogen bonds       : bond        0.05711 (  466)
  hydrogen bonds       : angle       4.14319 ( 1398)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.7419 (m-80) cc_final: 0.7042 (m-10)
REVERT: A  472 ARG cc_start: 0.7456 (mtt-85) cc_final: 0.7095 (ttm-80)
REVERT: A  504 HIS cc_start: 0.5910 (m-70) cc_final: 0.5515 (m-70)
REVERT: B  306 ASN cc_start: 0.7226 (t0) cc_final: 0.6998 (t0)
REVERT: B  357 PHE cc_start: 0.6776 (m-10) cc_final: 0.5580 (t80)
REVERT: B  411 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7538 (tm-30)
REVERT: B  472 ARG cc_start: 0.7074 (mtt180) cc_final: 0.6615 (mtp85)
REVERT: B  550 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7122 (tt0)
  outliers start: 12
  outliers final: 7
  residues processed: 65
  average time/residue: 1.0920
  time to fit residues: 75.3206
Evaluate side-chains
  59 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  445 TYR
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain B residue  401 ASN
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  581 SER
Chi-restraints excluded: chain B residue  584 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
B 387 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.130230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.100155 restraints weight = 23151.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.35
r_work: 0.3238 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6668  Z= 0.145
  Angle     :  0.474   5.728   9066  Z= 0.261
  Chirality :  0.036   0.169    986
  Planarity :  0.004   0.035   1080
  Dihedral  : 10.172  91.629   1046
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.67 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  2.81 (0.30), residues: 742
  helix:  2.68 (0.20), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.82 (0.45), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 293 
 TYR   0.018   0.001   TYR B 417 
 PHE   0.023   0.001   PHE A 605 
 TRP   0.009   0.001   TRP A 514 
 HIS   0.022   0.001   HIS B 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6666)
  covalent geometry    : angle       0.47286 ( 9062)
  SS BOND              : bond        0.00445 (    2)
  SS BOND              : angle       1.37072 (    4)
  hydrogen bonds       : bond        0.05635 (  466)
  hydrogen bonds       : angle       4.11289 ( 1398)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.7452 (m-80) cc_final: 0.7058 (m-10)
REVERT: A  504 HIS cc_start: 0.5964 (m-70) cc_final: 0.5596 (m-70)
REVERT: B  306 ASN cc_start: 0.7271 (t0) cc_final: 0.7052 (t0)
REVERT: B  357 PHE cc_start: 0.6822 (m-10) cc_final: 0.5635 (t80)
REVERT: B  472 ARG cc_start: 0.7146 (mtt180) cc_final: 0.6708 (mtp85)
REVERT: B  550 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7172 (tt0)
  outliers start: 11
  outliers final: 7
  residues processed: 65
  average time/residue: 1.0357
  time to fit residues: 71.9526
Evaluate side-chains
  61 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  445 TYR
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain B residue  518 TYR
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  581 SER
Chi-restraints excluded: chain B residue  584 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 3 optimal weight:    0.1980
   chunk 53 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 608 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.130737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.100688 restraints weight = 22928.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 2.35
r_work: 0.3243 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.3482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6668  Z= 0.135
  Angle     :  0.461   6.076   9066  Z= 0.254
  Chirality :  0.035   0.124    986
  Planarity :  0.004   0.034   1080
  Dihedral  :  9.873  86.333   1046
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.82 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  2.89 (0.30), residues: 742
  helix:  2.75 (0.20), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.83 (0.45), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 293 
 TYR   0.012   0.001   TYR B 368 
 PHE   0.022   0.001   PHE A 605 
 TRP   0.009   0.001   TRP A 514 
 HIS   0.008   0.001   HIS B 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6666)
  covalent geometry    : angle       0.46043 ( 9062)
  SS BOND              : bond        0.00436 (    2)
  SS BOND              : angle       1.35861 (    4)
  hydrogen bonds       : bond        0.05471 (  466)
  hydrogen bonds       : angle       4.06433 ( 1398)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.7447 (m-80) cc_final: 0.7069 (m-10)
REVERT: A  472 ARG cc_start: 0.7564 (ttm-80) cc_final: 0.7364 (ttm-80)
REVERT: A  504 HIS cc_start: 0.5954 (m-70) cc_final: 0.5557 (m-70)
REVERT: B  357 PHE cc_start: 0.6796 (m-10) cc_final: 0.5595 (t80)
REVERT: B  472 ARG cc_start: 0.7154 (mtt180) cc_final: 0.6719 (mtp85)
REVERT: B  550 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7198 (tt0)
  outliers start: 11
  outliers final: 6
  residues processed: 66
  average time/residue: 1.0309
  time to fit residues: 72.6207
Evaluate side-chains
  59 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  581 SER
Chi-restraints excluded: chain B residue  584 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 73 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 10 optimal weight:    0.3980
   chunk 66 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.130868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.100858 restraints weight = 23184.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 2.36
r_work: 0.3247 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.3598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6668  Z= 0.131
  Angle     :  0.458   5.765   9066  Z= 0.252
  Chirality :  0.035   0.123    986
  Planarity :  0.003   0.033   1080
  Dihedral  :  9.756  82.912   1046
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.02 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 16.82 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  2.96 (0.30), residues: 742
  helix:  2.80 (0.20), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.82 (0.45), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 293 
 TYR   0.020   0.001   TYR B 417 
 PHE   0.022   0.001   PHE A 605 
 TRP   0.009   0.001   TRP A 514 
 HIS   0.003   0.001   HIS B 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6666)
  covalent geometry    : angle       0.45697 ( 9062)
  SS BOND              : bond        0.00393 (    2)
  SS BOND              : angle       1.26884 (    4)
  hydrogen bonds       : bond        0.05368 (  466)
  hydrogen bonds       : angle       4.02211 ( 1398)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
REVERT: A  349 LEU cc_start: 0.8367 (tp) cc_final: 0.8112 (mm)
REVERT: A  357 PHE cc_start: 0.7435 (m-80) cc_final: 0.7064 (m-10)
REVERT: A  504 HIS cc_start: 0.5869 (m-70) cc_final: 0.5530 (m-70)
REVERT: B  357 PHE cc_start: 0.6788 (m-10) cc_final: 0.5582 (t80)
REVERT: B  472 ARG cc_start: 0.7164 (mtt180) cc_final: 0.6728 (mtp85)
REVERT: B  518 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.7689 (t80)
REVERT: B  538 ASP cc_start: 0.7287 (t0) cc_final: 0.6984 (t0)
REVERT: B  550 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7216 (tt0)
  outliers start: 10
  outliers final: 7
  residues processed: 65
  average time/residue: 1.0724
  time to fit residues: 74.3000
Evaluate side-chains
  62 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue  401 ASN
Chi-restraints excluded: chain B residue  518 TYR
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  581 SER
Chi-restraints excluded: chain B residue  584 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 62 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0670
   chunk 33 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.131323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.101351 restraints weight = 23325.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 2.35
r_work: 0.3251 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6668  Z= 0.126
  Angle     :  0.451   5.899   9066  Z= 0.249
  Chirality :  0.035   0.123    986
  Planarity :  0.004   0.065   1080
  Dihedral  :  9.641  81.860   1046
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 16.82 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  3.02 (0.30), residues: 742
  helix:  2.85 (0.20), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.85 (0.44), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 472 
 TYR   0.012   0.001   TYR B 518 
 PHE   0.021   0.001   PHE A 605 
 TRP   0.009   0.001   TRP B 514 
 HIS   0.002   0.001   HIS B 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6666)
  covalent geometry    : angle       0.45031 ( 9062)
  SS BOND              : bond        0.00417 (    2)
  SS BOND              : angle       1.32429 (    4)
  hydrogen bonds       : bond        0.05279 (  466)
  hydrogen bonds       : angle       3.99228 ( 1398)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
REVERT: A  349 LEU cc_start: 0.8338 (tp) cc_final: 0.8086 (mm)
REVERT: A  357 PHE cc_start: 0.7397 (m-80) cc_final: 0.7003 (m-10)
REVERT: A  504 HIS cc_start: 0.5927 (m-70) cc_final: 0.5595 (m-70)
REVERT: B  357 PHE cc_start: 0.6731 (m-10) cc_final: 0.5530 (t80)
REVERT: B  472 ARG cc_start: 0.7145 (mtt180) cc_final: 0.6710 (mtp85)
REVERT: B  518 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7561 (t80)
REVERT: B  538 ASP cc_start: 0.7282 (t0) cc_final: 0.6973 (t0)
REVERT: B  550 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7245 (tt0)
  outliers start: 9
  outliers final: 4
  residues processed: 67
  average time/residue: 1.0465
  time to fit residues: 74.8080
Evaluate side-chains
  62 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  588 SER
Chi-restraints excluded: chain B residue  518 TYR
Chi-restraints excluded: chain B residue  577 ILE
Chi-restraints excluded: chain B residue  584 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 19 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 608 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.130386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.100460 restraints weight = 23124.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 2.34
r_work: 0.3239 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.3722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6668  Z= 0.144
  Angle     :  0.467   5.930   9066  Z= 0.258
  Chirality :  0.035   0.126    986
  Planarity :  0.004   0.063   1080
  Dihedral  :  9.679  81.796   1046
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 17.27 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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:  2.94 (0.30), residues: 742
  helix:  2.80 (0.20), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.88 (0.44), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 472 
 TYR   0.023   0.001   TYR B 417 
 PHE   0.023   0.001   PHE A 605 
 TRP   0.009   0.001   TRP B 514 
 HIS   0.002   0.001   HIS B 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 6666)
  covalent geometry    : angle       0.46610 ( 9062)
  SS BOND              : bond        0.00441 (    2)
  SS BOND              : angle       1.29511 (    4)
  hydrogen bonds       : bond        0.05485 (  466)
  hydrogen bonds       : angle       4.03147 ( 1398)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4843.78 seconds
wall clock time: 82 minutes 47.76 seconds (4967.76 seconds total)