Starting phenix.real_space_refine
on Thu May 15 09:36:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dvj_47208/05_2025/9dvj_47208_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dvj_47208/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dvj_47208/05_2025/9dvj_47208.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dvj_47208/05_2025/9dvj_47208.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dvj_47208/05_2025/9dvj_47208_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dvj_47208/05_2025/9dvj_47208_trim.cif"
  }
  resolution = 2.52
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.023
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.08, per 1000 atoms: 0.56
  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: 3.31
  Conformation dependent library (CDL) restraints added in 963.8 milliseconds
  

  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: 0.79
  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: 4.34

  Time building geometry restraints manager: 3.95 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: 0.02
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:             2.670
  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:             0.210
  Extract box with map and model:          0.500
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     29.790
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.610
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.78 (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
 TRP   0.009   0.001   TRP B 327 
 HIS   0.002   0.000   HIS B 499 
 PHE   0.013   0.001   PHE A 610 
 TYR   0.009   0.001   TYR A 496 
 ARG   0.006   0.000   ARG B 380 

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

*********************** 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  : 0.923 
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: 0.5803 (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: 1.6123
  time to fit residues: 186.1082
Evaluate side-chains
  62 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
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 62 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0670
   chunk 29 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.6518

-------------------------------------------------------------------------------
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 = 0.3860 r_free = 0.3860 target = 0.143987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.114894 restraints weight = 22780.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.34
r_work: 0.3430 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.1500

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     :  0.476   5.129   9066  Z= 0.256
  Chirality :  0.036   0.125    986
  Planarity :  0.004   0.041   1080
  Dihedral  : 12.227 116.413   1052
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 16.07 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.47 (0.30), residues: 742
  helix:  3.17 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -1.66 (0.44), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 327 
 HIS   0.006   0.001   HIS B 499 
 PHE   0.018   0.001   PHE A 605 
 TYR   0.011   0.001   TYR A 352 
 ARG   0.005   0.000   ARG A 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04934 (  466)
  hydrogen bonds       : angle       4.12504 ( 1398)
  SS BOND              : bond        0.00272 (    2)
  SS BOND              : angle       1.03211 (    4)
  covalent geometry    : bond        0.00300 ( 6666)
  covalent geometry    : angle       0.47590 ( 9062)

*********************** 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
  75 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.7350 (m-80) cc_final: 0.7002 (m-10)
REVERT: A  386 PHE cc_start: 0.8097 (m-10) cc_final: 0.7881 (m-10)
REVERT: A  539 LYS cc_start: 0.7974 (pttt) cc_final: 0.7209 (mmtm)
REVERT: A  550 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6941 (mt-10)
REVERT: B  411 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7752 (tm-30)
REVERT: B  472 ARG cc_start: 0.6712 (mtt180) cc_final: 0.6235 (mtp85)
REVERT: B  510 PHE cc_start: 0.7325 (m-10) cc_final: 0.7096 (m-80)
REVERT: B  550 GLU cc_start: 0.7694 (mm-30) cc_final: 0.6996 (tt0)
  outliers start: 9
  outliers final: 3
  residues processed: 74
  average time/residue: 1.7021
  time to fit residues: 136.4449
Evaluate side-chains
  62 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  578 SER
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain B residue  609 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.3725 r_free = 0.3725 target = 0.130799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.101509 restraints weight = 23596.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.33
r_work: 0.3255 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6668  Z= 0.193
  Angle     :  0.537   7.273   9066  Z= 0.295
  Chirality :  0.038   0.131    986
  Planarity :  0.004   0.059   1080
  Dihedral  : 11.784 113.857   1050
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.71 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.30), residues: 742
  helix:  2.63 (0.20), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.92 (0.44), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 327 
 HIS   0.004   0.001   HIS B 499 
 PHE   0.032   0.002   PHE A 605 
 TYR   0.015   0.002   TYR B 417 
 ARG   0.004   0.001   ARG A 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06481 (  466)
  hydrogen bonds       : angle       4.31308 ( 1398)
  SS BOND              : bond        0.00476 (    2)
  SS BOND              : angle       1.27505 (    4)
  covalent geometry    : bond        0.00428 ( 6666)
  covalent geometry    : angle       0.53614 ( 9062)

*********************** 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
  85 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.7464 (m-80) cc_final: 0.7060 (m-10)
REVERT: A  472 ARG cc_start: 0.7463 (mtt-85) cc_final: 0.7191 (ttm-80)
REVERT: A  507 THR cc_start: 0.6630 (OUTLIER) cc_final: 0.6416 (m)
REVERT: A  550 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7173 (mt-10)
REVERT: B  306 ASN cc_start: 0.7046 (t0) cc_final: 0.6703 (t0)
REVERT: B  411 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7823 (tm-30)
REVERT: B  469 ASP cc_start: 0.7757 (m-30) cc_final: 0.7543 (m-30)
REVERT: B  472 ARG cc_start: 0.7003 (mtt180) cc_final: 0.6538 (mtp85)
REVERT: B  529 ASP cc_start: 0.7750 (m-30) cc_final: 0.7515 (m-30)
REVERT: B  550 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7087 (tt0)
REVERT: B  613 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8579 (tm-30)
  outliers start: 16
  outliers final: 2
  residues processed: 82
  average time/residue: 1.7132
  time to fit residues: 151.1019
Evaluate side-chains
  59 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  498 THR
Chi-restraints excluded: chain A residue  507 THR
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 20 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 608 ASN
B 441 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.131657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.101988 restraints weight = 22922.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 2.30
r_work: 0.3267 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.2929

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= 0.152
  Angle     :  0.476   5.083   9066  Z= 0.264
  Chirality :  0.036   0.166    986
  Planarity :  0.004   0.046   1080
  Dihedral  : 11.279 109.384   1046
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.80 (0.30), residues: 742
  helix:  2.69 (0.20), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.92 (0.44), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 327 
 HIS   0.005   0.001   HIS B 441 
 PHE   0.026   0.001   PHE A 605 
 TYR   0.014   0.001   TYR B 368 
 ARG   0.004   0.000   ARG A 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05791 (  466)
  hydrogen bonds       : angle       4.18683 ( 1398)
  SS BOND              : bond        0.00479 (    2)
  SS BOND              : angle       1.54691 (    4)
  covalent geometry    : bond        0.00330 ( 6666)
  covalent geometry    : angle       0.47469 ( 9062)

*********************** 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
  73 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.7506 (m-80) cc_final: 0.7109 (m-10)
REVERT: A  386 PHE cc_start: 0.8252 (m-10) cc_final: 0.8039 (m-10)
REVERT: A  472 ARG cc_start: 0.7465 (mtt-85) cc_final: 0.7107 (ttm-80)
REVERT: A  504 HIS cc_start: 0.6029 (m-70) cc_final: 0.5647 (m-70)
REVERT: A  550 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7224 (mt-10)
REVERT: B  306 ASN cc_start: 0.7195 (t0) cc_final: 0.6826 (t0)
REVERT: B  411 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7655 (tm-30)
REVERT: B  469 ASP cc_start: 0.7671 (m-30) cc_final: 0.7450 (m-30)
REVERT: B  472 ARG cc_start: 0.7053 (mtt180) cc_final: 0.6609 (mtp85)
REVERT: B  550 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7070 (tt0)
  outliers start: 11
  outliers final: 5
  residues processed: 71
  average time/residue: 2.1118
  time to fit residues: 159.7481
Evaluate side-chains
  61 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
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  584 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 34 optimal weight:    0.3980
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 608 ASN
B 441 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.130616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.100552 restraints weight = 23162.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 2.34
r_work: 0.3240 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.3190

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= 0.159
  Angle     :  0.478   5.042   9066  Z= 0.265
  Chirality :  0.036   0.126    986
  Planarity :  0.004   0.052   1080
  Dihedral  : 10.828  99.375   1046
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 16.67 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.77 (0.30), residues: 742
  helix:  2.67 (0.20), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.90 (0.44), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 514 
 HIS   0.003   0.001   HIS B 476 
 PHE   0.025   0.002   PHE A 605 
 TYR   0.014   0.001   TYR B 417 
 ARG   0.004   0.000   ARG A 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05804 (  466)
  hydrogen bonds       : angle       4.15570 ( 1398)
  SS BOND              : bond        0.00473 (    2)
  SS BOND              : angle       1.43173 (    4)
  covalent geometry    : bond        0.00353 ( 6666)
  covalent geometry    : angle       0.47740 ( 9062)

*********************** 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  : 0.976 
Fit side-chains
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.7430 (m-80) cc_final: 0.7053 (m-10)
REVERT: A  386 PHE cc_start: 0.8342 (m-10) cc_final: 0.8139 (m-10)
REVERT: A  472 ARG cc_start: 0.7452 (mtt-85) cc_final: 0.7079 (ttm-80)
REVERT: A  504 HIS cc_start: 0.5904 (m-70) cc_final: 0.5567 (m-70)
REVERT: A  550 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7220 (mt-10)
REVERT: B  306 ASN cc_start: 0.7259 (t0) cc_final: 0.7021 (t0)
REVERT: B  357 PHE cc_start: 0.6778 (m-10) cc_final: 0.5581 (t80)
REVERT: B  411 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7530 (tm-30)
REVERT: B  469 ASP cc_start: 0.7686 (m-30) cc_final: 0.7452 (m-30)
REVERT: B  472 ARG cc_start: 0.7040 (mtt180) cc_final: 0.6589 (mtp85)
REVERT: B  550 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7078 (tt0)
  outliers start: 10
  outliers final: 7
  residues processed: 69
  average time/residue: 2.1683
  time to fit residues: 159.0117
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  : 0.976 
-------------------------------------------------------------------------------
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 49 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 24 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0980
   chunk 67 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 608 ASN
B 441 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.131975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.101547 restraints weight = 23169.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 2.38
r_work: 0.3253 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.3212

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= 0.129
  Angle     :  0.467   5.653   9066  Z= 0.257
  Chirality :  0.035   0.145    986
  Planarity :  0.004   0.050   1080
  Dihedral  : 10.564  95.434   1046
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 16.67 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.90 (0.30), residues: 742
  helix:  2.77 (0.20), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.88 (0.44), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 327 
 HIS   0.022   0.001   HIS B 504 
 PHE   0.022   0.001   PHE A 605 
 TYR   0.012   0.001   TYR B 368 
 ARG   0.005   0.000   ARG A 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05454 (  466)
  hydrogen bonds       : angle       4.07203 ( 1398)
  SS BOND              : bond        0.00407 (    2)
  SS BOND              : angle       1.36923 (    4)
  covalent geometry    : bond        0.00271 ( 6666)
  covalent geometry    : angle       0.46630 ( 9062)

*********************** 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
  63 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.7431 (m-80) cc_final: 0.7048 (m-10)
REVERT: A  386 PHE cc_start: 0.8299 (m-10) cc_final: 0.8092 (m-10)
REVERT: A  472 ARG cc_start: 0.7471 (mtt-85) cc_final: 0.7120 (ttm-80)
REVERT: A  504 HIS cc_start: 0.5941 (m-70) cc_final: 0.5567 (m-70)
REVERT: B  306 ASN cc_start: 0.7253 (t0) cc_final: 0.7023 (t0)
REVERT: B  357 PHE cc_start: 0.6796 (m-10) cc_final: 0.5608 (t80)
REVERT: B  469 ASP cc_start: 0.7746 (m-30) cc_final: 0.7488 (m-30)
REVERT: B  472 ARG cc_start: 0.7080 (mtt180) cc_final: 0.6639 (mtp85)
REVERT: B  550 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7125 (tt0)
  outliers start: 12
  outliers final: 7
  residues processed: 62
  average time/residue: 2.0126
  time to fit residues: 133.6808
Evaluate side-chains
  58 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
A 608 ASN
B 387 HIS
B 401 ASN
B 441 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.127631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.097560 restraints weight = 23144.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 2.33
r_work: 0.3198 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3079 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.3579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6668  Z= 0.197
  Angle     :  0.522   5.573   9066  Z= 0.290
  Chirality :  0.037   0.132    986
  Planarity :  0.004   0.059   1080
  Dihedral  : 10.414  89.856   1046
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 16.97 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (0.30), residues: 742
  helix:  2.47 (0.20), residues: 596
  sheet:  None (None), residues: 0
  loop : -1.91 (0.45), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 514 
 HIS   0.021   0.002   HIS B 504 
 PHE   0.030   0.002   PHE A 605 
 TYR   0.018   0.002   TYR B 417 
 ARG   0.005   0.001   ARG A 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06321 (  466)
  hydrogen bonds       : angle       4.27403 ( 1398)
  SS BOND              : bond        0.00579 (    2)
  SS BOND              : angle       1.52073 (    4)
  covalent geometry    : bond        0.00446 ( 6666)
  covalent geometry    : angle       0.52079 ( 9062)

*********************** 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
  69 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.7482 (m-80) cc_final: 0.7074 (m-10)
REVERT: A  504 HIS cc_start: 0.5944 (m-70) cc_final: 0.5591 (m-70)
REVERT: B  357 PHE cc_start: 0.6847 (m-10) cc_final: 0.5694 (t80)
REVERT: B  472 ARG cc_start: 0.7186 (mtt180) cc_final: 0.6715 (mtp85)
REVERT: B  538 ASP cc_start: 0.7228 (t0) cc_final: 0.6946 (t0)
REVERT: B  550 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7165 (tt0)
  outliers start: 10
  outliers final: 6
  residues processed: 67
  average time/residue: 1.9320
  time to fit residues: 138.3224
Evaluate side-chains
  60 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   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 314 GLN
A 608 ASN
B 401 ASN
B 441 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.129594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.099667 restraints weight = 23280.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 2.34
r_work: 0.3229 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.3647

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= 0.138
  Angle     :  0.476   5.932   9066  Z= 0.262
  Chirality :  0.036   0.124    986
  Planarity :  0.004   0.056   1080
  Dihedral  : 10.052  86.257   1046
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 17.12 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.30), residues: 742
  helix:  2.60 (0.20), residues: 596
  sheet:  None (None), residues: 0
  loop : -1.86 (0.45), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 514 
 HIS   0.003   0.001   HIS B 504 
 PHE   0.025   0.001   PHE A 605 
 TYR   0.010   0.001   TYR A 352 
 ARG   0.006   0.000   ARG A 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05721 (  466)
  hydrogen bonds       : angle       4.12829 ( 1398)
  SS BOND              : bond        0.00449 (    2)
  SS BOND              : angle       1.40426 (    4)
  covalent geometry    : bond        0.00292 ( 6666)
  covalent geometry    : angle       0.47503 ( 9062)

*********************** 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  : 0.972 
Fit side-chains
   revert: symmetry clash
REVERT: A  357 PHE cc_start: 0.7434 (m-80) cc_final: 0.7036 (m-10)
REVERT: A  472 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.7337 (ttm-80)
REVERT: A  504 HIS cc_start: 0.5963 (m-70) cc_final: 0.5607 (m-70)
REVERT: B  357 PHE cc_start: 0.6791 (m-10) cc_final: 0.5618 (t80)
REVERT: B  472 ARG cc_start: 0.7182 (mtt180) cc_final: 0.6729 (mtp85)
REVERT: B  538 ASP cc_start: 0.7256 (t0) cc_final: 0.6964 (t0)
REVERT: B  550 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7160 (tt0)
  outliers start: 11
  outliers final: 6
  residues processed: 66
  average time/residue: 1.9340
  time to fit residues: 136.5739
Evaluate side-chains
  58 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  550 GLU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
A 314 GLN
A 608 ASN
B 401 ASN
B 441 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.128034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.097822 restraints weight = 23292.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.37
r_work: 0.3202 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3083 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.3835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6668  Z= 0.175
  Angle     :  0.496   5.399   9066  Z= 0.275
  Chirality :  0.037   0.130    986
  Planarity :  0.004   0.058   1080
  Dihedral  : 10.123  85.029   1046
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 16.97 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.30), residues: 742
  helix:  2.50 (0.20), residues: 596
  sheet:  None (None), residues: 0
  loop : -1.88 (0.45), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 514 
 HIS   0.003   0.001   HIS B 387 
 PHE   0.027   0.002   PHE A 605 
 TYR   0.021   0.002   TYR B 417 
 ARG   0.007   0.001   ARG A 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06081 (  466)
  hydrogen bonds       : angle       4.20233 ( 1398)
  SS BOND              : bond        0.00532 (    2)
  SS BOND              : angle       1.53473 (    4)
  covalent geometry    : bond        0.00395 ( 6666)
  covalent geometry    : angle       0.49473 ( 9062)

*********************** 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: 12
    poor density    : 54
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
REVERT: A  349 LEU cc_start: 0.8370 (tp) cc_final: 0.8098 (mm)
REVERT: A  357 PHE cc_start: 0.7457 (m-80) cc_final: 0.7066 (m-10)
REVERT: A  472 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7491 (ttm-80)
REVERT: A  504 HIS cc_start: 0.5944 (m-70) cc_final: 0.5605 (m-70)
REVERT: B  357 PHE cc_start: 0.6842 (m-10) cc_final: 0.5669 (t80)
REVERT: B  472 ARG cc_start: 0.7251 (mtt180) cc_final: 0.6786 (mtp85)
REVERT: B  538 ASP cc_start: 0.7379 (t0) cc_final: 0.7079 (t0)
REVERT: B  550 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7229 (tt0)
  outliers start: 12
  outliers final: 9
  residues processed: 65
  average time/residue: 1.9326
  time to fit residues: 134.7494
Evaluate side-chains
  63 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  486 THR
Chi-restraints excluded: chain A residue  550 GLU
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain B residue  401 ASN
Chi-restraints excluded: chain B residue  504 HIS
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 49 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0000
   chunk 55 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 59 optimal weight:    0.1980
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 608 ASN
B 401 ASN
B 441 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.128215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.098131 restraints weight = 23260.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 2.36
r_work: 0.3207 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.3817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.153   6668  Z= 0.209
  Angle     :  0.921  59.173   9066  Z= 0.568
  Chirality :  0.036   0.137    986
  Planarity :  0.004   0.058   1080
  Dihedral  : 10.117  85.171   1046
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 17.12 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.59 (0.30), residues: 742
  helix:  2.51 (0.20), residues: 596
  sheet:  None (None), residues: 0
  loop : -1.88 (0.45), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 514 
 HIS   0.003   0.001   HIS B 299 
 PHE   0.027   0.001   PHE A 605 
 TYR   0.015   0.001   TYR B 417 
 ARG   0.004   0.000   ARG A 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05986 (  466)
  hydrogen bonds       : angle       4.20603 ( 1398)
  SS BOND              : bond        0.00530 (    2)
  SS BOND              : angle       1.49277 (    4)
  covalent geometry    : bond        0.00443 ( 6666)
  covalent geometry    : angle       0.92053 ( 9062)

********************** 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
  65 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
REVERT: A  349 LEU cc_start: 0.8369 (tp) cc_final: 0.8096 (mm)
REVERT: A  357 PHE cc_start: 0.7452 (m-80) cc_final: 0.7061 (m-10)
REVERT: A  472 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7495 (ttm-80)
REVERT: A  504 HIS cc_start: 0.5944 (m-70) cc_final: 0.5605 (m-70)
REVERT: B  357 PHE cc_start: 0.6830 (m-10) cc_final: 0.5659 (t80)
REVERT: B  472 ARG cc_start: 0.7251 (mtt180) cc_final: 0.6787 (mtp85)
REVERT: B  538 ASP cc_start: 0.7381 (t0) cc_final: 0.7082 (t0)
REVERT: B  550 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7223 (tt0)
  outliers start: 11
  outliers final: 7
  residues processed: 63
  average time/residue: 1.9113
  time to fit residues: 129.3022
Evaluate side-chains
  60 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  486 THR
Chi-restraints excluded: chain A residue  550 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 608 ASN
B 441 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.128180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.097979 restraints weight = 23308.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 2.37
r_work: 0.3205 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.153   6668  Z= 0.209
  Angle     :  0.921  59.199   9066  Z= 0.568
  Chirality :  0.036   0.136    986
  Planarity :  0.004   0.058   1080
  Dihedral  : 10.117  85.171   1046
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 17.27 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.59 (0.30), residues: 742
  helix:  2.51 (0.20), residues: 596
  sheet:  None (None), residues: 0
  loop : -1.88 (0.45), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 514 
 HIS   0.003   0.001   HIS B 299 
 PHE   0.027   0.001   PHE A 605 
 TYR   0.015   0.001   TYR B 417 
 ARG   0.004   0.000   ARG A 293 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05986 (  466)
  hydrogen bonds       : angle       4.20601 ( 1398)
  SS BOND              : bond        0.00530 (    2)
  SS BOND              : angle       1.49282 (    4)
  covalent geometry    : bond        0.00443 ( 6666)
  covalent geometry    : angle       0.92060 ( 9062)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8705.73 seconds
wall clock time: 149 minutes 28.16 seconds (8968.16 seconds total)