Starting phenix.real_space_refine
on Thu Sep 18 01:55:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dvk_47209/09_2025/9dvk_47209_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dvk_47209/09_2025/9dvk_47209.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dvk_47209/09_2025/9dvk_47209_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dvk_47209/09_2025/9dvk_47209_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dvk_47209/09_2025/9dvk_47209.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dvk_47209/09_2025/9dvk_47209.map"
  }
  resolution = 3.06
  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=   0.021
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    4412      2.51       5
     N    1015      2.21       5
     O    1057      1.98       5
     H    6319      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 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: 12839
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 378, 6292
          Classifications: {'peptide': 378}
          Link IDs: {'PTRANS': 13, 'TRANS': 364}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 6364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 6364
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 12, 'TRANS': 369}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 126
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 126
          Unusual residues: {'CLR': 1, 'CPL': 2, 'PO4': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 9
    Chain: "B"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 57
          Unusual residues: {'CPL': 1, 'PO4': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.83, per 1000 atoms: 0.22
  Number of scatterers: 12839
  At special positions: 0
  Unit cell: (73.4695, 72.644, 118.047, 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    1057      8.00
     N    1015      7.00
     C    4412      6.00
     H    6319      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: 1.28
  Conformation dependent library (CDL) restraints added in 502.2 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1444

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      80.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 230 through 258
    Processing helix  chain 'A' and resid 267 through 296
      removed outlier: 4.401A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 4.575A  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: 4.031A  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 471
      removed outlier: 3.512A  pdb=" N   ALA A 449 " --> pdb=" O   TYR A 445 " (cutoff:3.500A)
      Proline residue:  A 455  - end of helix
    Processing helix  chain 'A' and resid 472 through 502
      removed outlier: 3.998A  pdb=" N   HIS A 476 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 3.844A  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: 4.023A  pdb=" N   TYR A 559 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
      removed outlier: 3.861A  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 231 through 259
    Processing helix  chain 'B' and resid 265 through 296
      removed outlier: 3.932A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.394A  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
      removed outlier: 4.177A  pdb=" N   LEU B 349 " --> pdb=" O   TYR B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 383
      removed outlier: 3.603A  pdb=" N   ARG B 371 " --> pdb=" O   TYR B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 403
    Processing helix  chain 'B' and resid 403 through 420
      removed outlier: 3.598A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.670A  pdb=" N   TYR B 443 " --> pdb=" O   ILE B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 445 through 471
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'B' and resid 472 through 502
      removed outlier: 4.064A  pdb=" N   HIS B 476 " --> pdb=" O   ARG B 472 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   VAL B 478 " --> pdb=" O   PHE B 474 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   ASN B 479 " --> pdb=" O   PRO B 475 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 531
    Processing helix  chain 'B' and resid 555 through 582
      removed outlier: 4.148A  pdb=" N   TYR B 559 " --> pdb=" O   GLN B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 618
      removed outlier: 4.358A  pdb=" N   ILE B 591 " --> pdb=" O   HIS B 587 " (cutoff:3.500A)
      Proline residue:  B 598  - end of helix

    468 hydrogen bonds defined for protein.
    1404 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: 2.96

  Time building geometry restraints manager: 1.79 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 6303
        1.03 -     1.23: 26
        1.23 -     1.42: 2968
        1.42 -     1.62: 3704
        1.62 -     1.81: 48
  Bond restraints: 13049
  Sorted by residual:
  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 2.88e+01
  bond pdb=" O3P CPL B 802 "
       pdb=" P   CPL B 802 "
    ideal  model  delta    sigma   weight residual
    1.633  1.740 -0.107 2.00e-02 2.50e+03 2.85e+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 1.10e+01
  bond pdb=" O4P CPL B 802 "
       pdb=" P   CPL B 802 "
    ideal  model  delta    sigma   weight residual
    1.648  1.713 -0.065 2.00e-02 2.50e+03 1.07e+01
  bond pdb=" N   TRP B 534 "
       pdb=" H   TRP B 534 "
    ideal  model  delta    sigma   weight residual
    0.860  0.913 -0.053 2.00e-02 2.50e+03 7.04e+00
  ... (remaining 13044 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.05: 23275
        3.05 -     6.09: 72
        6.09 -     9.14: 10
        9.14 -    12.19: 6
       12.19 -    15.24: 2
  Bond angle restraints: 23365
  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 802 "
        pdb=" P   CPL B 802 "
        pdb=" O2P CPL B 802 "
      ideal   model   delta    sigma   weight residual
     119.55  134.72  -15.17 3.00e+00 1.11e-01 2.56e+01
  angle pdb=" CA  TYR B 352 "
        pdb=" C   TYR B 352 "
        pdb=" O   TYR B 352 "
      ideal   model   delta    sigma   weight residual
     119.97  115.46    4.51 1.15e+00 7.56e-01 1.54e+01
  angle pdb=" CA  TRP B 534 "
        pdb=" C   TRP B 534 "
        pdb=" O   TRP B 534 "
      ideal   model   delta    sigma   weight residual
     120.42  116.51    3.91 1.06e+00 8.90e-01 1.36e+01
  angle pdb=" N   TYR A 352 "
        pdb=" CA  TYR A 352 "
        pdb=" C   TYR A 352 "
      ideal   model   delta    sigma   weight residual
     111.71  107.60    4.11 1.15e+00 7.56e-01 1.28e+01
  ... (remaining 23360 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.51: 5995
       32.51 -    65.01: 260
       65.01 -    97.52: 16
       97.52 -   130.02: 2
      130.02 -   162.53: 4
  Dihedral angle restraints: 6277
    sinusoidal: 3264
      harmonic: 3013
  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  -90.44  162.53     1      3.00e+01 1.11e-03 2.08e+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  148.89  160.29     1      3.00e+01 1.11e-03 2.07e+01
  dihedral pdb=" C3  CPL B 802 "
           pdb=" C1  CPL B 802 "
           pdb=" C2  CPL B 802 "
           pdb=" O3P CPL B 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
      72.09  -68.45  140.54     1      3.00e+01 1.11e-03 1.89e+01
  ... (remaining 6274 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 908
       0.073 -    0.147: 72
       0.147 -    0.220: 0
       0.220 -    0.294: 1
       0.294 -    0.367: 6
  Chirality restraints: 987
  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 3.37e+00
  chirality pdb=" C2  CPL B 802 "
            pdb=" C1  CPL B 802 "
            pdb=" C3  CPL B 802 "
            pdb=" O2  CPL B 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.65    0.34 2.00e-01 2.50e+01 2.82e+00
  chirality pdb=" C2  CPL A 803 "
            pdb=" C1  CPL A 803 "
            pdb=" C3  CPL A 803 "
            pdb=" O2  CPL A 803 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.65    0.33 2.00e-01 2.50e+01 2.79e+00
  ... (remaining 984 not shown)

  Planarity restraints: 1823
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 479 "    0.095 2.00e-02 2.50e+03   9.73e-02 1.42e+02
        pdb=" CG  ASN A 479 "   -0.014 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 479 "   -0.084 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 479 "   -0.007 2.00e-02 2.50e+03
        pdb="HD21 ASN A 479 "    0.148 2.00e-02 2.50e+03
        pdb="HD22 ASN A 479 "   -0.137 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 482 "    0.013 2.00e-02 2.50e+03   2.49e-02 6.21e+00
        pdb=" N   TYR A 483 "   -0.043 2.00e-02 2.50e+03
        pdb=" CA  TYR A 483 "    0.011 2.00e-02 2.50e+03
        pdb=" H   TYR A 483 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 534 "    0.012 2.00e-02 2.50e+03   2.46e-02 6.04e+00
        pdb=" C   TRP B 534 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   TRP B 534 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLY B 535 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1820 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.21: 1000
        2.21 -     2.81: 26695
        2.81 -     3.41: 37827
        3.41 -     4.00: 47721
        4.00 -     4.60: 73888
  Nonbonded interactions: 187131
  Sorted by model distance:
  nonbonded pdb=" HB2 GLU B 550 "
            pdb="HD21 LEU B 617 "
     model   vdw
     1.618 2.440
  nonbonded pdb="HH12 ARG A 548 "
            pdb=" OE2 GLU A 613 "
     model   vdw
     1.661 2.450
  nonbonded pdb=" OG  SER A 402 "
            pdb=" HE  ARG A 604 "
     model   vdw
     1.668 2.450
  nonbonded pdb="HH12 ARG B 466 "
            pdb=" O   GLY B 621 "
     model   vdw
     1.692 2.450
  nonbonded pdb="HD21 ASN B 361 "
            pdb=" HG1 THR B 363 "
     model   vdw
     1.717 2.100
  ... (remaining 187126 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 230 through 801)
  selection = (chain 'B' and (resid 230 through 258 or (resid 265 and (name N or name CA or na \ 
me C or name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name \ 
 HB or name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD1 \ 
1 or name HD12 or name HD13)) or resid 266 through 801))
}

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:             3.630
  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:             0.080
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.880
  Find NCS groups from input model:        0.190
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
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   6732  Z= 0.224
  Angle     :  0.676  15.237   9132  Z= 0.319
  Chirality :  0.044   0.367    987
  Planarity :  0.003   0.029   1093
  Dihedral  : 17.965 162.531   2437
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 15.16 %
    Favored  : 84.10 %
  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:  3.52 (0.30), residues: 750
  helix:  3.29 (0.20), residues: 584
  sheet:  None (None), residues: 0
  loop : -1.53 (0.39), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 472 
 TYR   0.037   0.001   TYR A 352 
 PHE   0.017   0.001   PHE B 322 
 TRP   0.013   0.001   TRP A 573 
 HIS   0.003   0.001   HIS B 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 6730)
  covalent geometry    : angle       0.67648 ( 9128)
  SS BOND              : bond        0.00178 (    2)
  SS BOND              : angle       0.36117 (    4)
  hydrogen bonds       : bond        0.09876 (  468)
  hydrogen bonds       : angle       4.38584 ( 1404)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 138
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 ASN cc_start: 0.7238 (t0) cc_final: 0.6854 (m-40)
REVERT: A  468 ARG cc_start: 0.6795 (ttt180) cc_final: 0.6528 (ttm170)
REVERT: A  471 LYS cc_start: 0.7832 (ttmm) cc_final: 0.7561 (tppt)
REVERT: A  624 ARG cc_start: 0.7524 (mtm110) cc_final: 0.7258 (mtm-85)
REVERT: B  272 TYR cc_start: 0.7642 (m-80) cc_final: 0.7296 (m-80)
REVERT: B  318 GLU cc_start: 0.6568 (mt-10) cc_final: 0.5955 (mm-30)
REVERT: B  347 TYR cc_start: 0.7030 (m-80) cc_final: 0.6725 (m-80)
REVERT: B  354 PHE cc_start: 0.8291 (t80) cc_final: 0.7979 (t80)
REVERT: B  394 PHE cc_start: 0.6584 (OUTLIER) cc_final: 0.5294 (p90)
REVERT: B  465 ARG cc_start: 0.8136 (tpt-90) cc_final: 0.7842 (tpt170)
  outliers start: 5
  outliers final: 4
  residues processed: 143
  average time/residue: 0.1881
  time to fit residues: 35.5863
Evaluate side-chains
  115 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 110
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  609 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 310 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.183152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.151909 restraints weight = 22743.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3799 rms_B_bonded: 2.37
r_work: 0.3689 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6732  Z= 0.163
  Angle     :  0.521   4.542   9132  Z= 0.283
  Chirality :  0.037   0.135    987
  Planarity :  0.005   0.034   1093
  Dihedral  : 15.405 158.886   1033
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.75 %
    Favored  : 81.72 %
  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:  3.11 (0.30), residues: 750
  helix:  2.98 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -1.87 (0.37), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 466 
 TYR   0.022   0.002   TYR B 445 
 PHE   0.019   0.001   PHE A 605 
 TRP   0.015   0.002   TRP B 573 
 HIS   0.007   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 6730)
  covalent geometry    : angle       0.52096 ( 9128)
  SS BOND              : bond        0.00374 (    2)
  SS BOND              : angle       1.03592 (    4)
  hydrogen bonds       : bond        0.04913 (  468)
  hydrogen bonds       : angle       4.04638 ( 1404)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 PHE cc_start: 0.7558 (m-10) cc_final: 0.7297 (m-10)
REVERT: A  401 ASN cc_start: 0.7730 (t0) cc_final: 0.7042 (m-40)
REVERT: A  468 ARG cc_start: 0.6515 (ttt180) cc_final: 0.6174 (ttm170)
REVERT: A  624 ARG cc_start: 0.7613 (mtm110) cc_final: 0.7358 (mtm-85)
REVERT: B  318 GLU cc_start: 0.6625 (mt-10) cc_final: 0.5893 (mm-30)
REVERT: B  565 GLU cc_start: 0.8709 (pp20) cc_final: 0.8459 (pp20)
  outliers start: 17
  outliers final: 13
  residues processed: 114
  average time/residue: 0.2192
  time to fit residues: 32.4119
Evaluate side-chains
  104 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  304 GLU
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  609 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   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 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 462 GLN
** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.177877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.146828 restraints weight = 23104.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 2.35
r_work: 0.3627 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6732  Z= 0.155
  Angle     :  0.484   4.384   9132  Z= 0.265
  Chirality :  0.035   0.136    987
  Planarity :  0.004   0.035   1093
  Dihedral  : 15.201 164.419   1031
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.90 %
    Favored  : 81.43 %
  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:  2.97 (0.30), residues: 750
  helix:  2.88 (0.20), residues: 593
  sheet:  None (None), residues: 0
  loop : -1.93 (0.39), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 273 
 TYR   0.011   0.001   TYR B 518 
 PHE   0.022   0.001   PHE A 605 
 TRP   0.014   0.002   TRP B 573 
 HIS   0.005   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 6730)
  covalent geometry    : angle       0.48338 ( 9128)
  SS BOND              : bond        0.00396 (    2)
  SS BOND              : angle       0.94586 (    4)
  hydrogen bonds       : bond        0.05238 (  468)
  hydrogen bonds       : angle       4.04086 ( 1404)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 PHE cc_start: 0.7774 (m-10) cc_final: 0.7506 (m-10)
REVERT: A  468 ARG cc_start: 0.6581 (ttt180) cc_final: 0.6253 (ttm170)
REVERT: A  550 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6648 (mt-10)
REVERT: A  624 ARG cc_start: 0.7616 (mtm110) cc_final: 0.7039 (mtm-85)
REVERT: B  318 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6097 (mm-30)
REVERT: B  347 TYR cc_start: 0.7265 (m-80) cc_final: 0.6728 (m-80)
REVERT: B  565 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8593 (pp20)
  outliers start: 18
  outliers final: 12
  residues processed: 109
  average time/residue: 0.2154
  time to fit residues: 30.4173
Evaluate side-chains
  104 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  504 HIS
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain B residue  565 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0270
   chunk 58 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
B 248 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.176886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.146106 restraints weight = 22784.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 2.31
r_work: 0.3591 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6732  Z= 0.141
  Angle     :  0.475   5.205   9132  Z= 0.261
  Chirality :  0.035   0.137    987
  Planarity :  0.004   0.041   1093
  Dihedral  : 14.279 160.628   1027
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 15.30 %
    Favored  : 81.87 %
  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: 750
  helix:  2.84 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.05 (0.37), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 465 
 TYR   0.012   0.001   TYR B 518 
 PHE   0.020   0.001   PHE A 605 
 TRP   0.013   0.001   TRP B 573 
 HIS   0.007   0.001   HIS B 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6730)
  covalent geometry    : angle       0.47471 ( 9128)
  SS BOND              : bond        0.00388 (    2)
  SS BOND              : angle       1.04867 (    4)
  hydrogen bonds       : bond        0.05029 (  468)
  hydrogen bonds       : angle       3.97483 ( 1404)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 PHE cc_start: 0.7820 (m-10) cc_final: 0.7567 (m-10)
REVERT: A  468 ARG cc_start: 0.6559 (ttt180) cc_final: 0.6210 (ttm170)
REVERT: A  550 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6784 (mt-10)
REVERT: A  624 ARG cc_start: 0.7653 (mtm110) cc_final: 0.7202 (mtm-85)
REVERT: B  293 ARG cc_start: 0.7717 (mmm-85) cc_final: 0.6520 (ttm170)
REVERT: B  318 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6211 (mm-30)
REVERT: B  347 TYR cc_start: 0.7343 (m-80) cc_final: 0.6806 (m-80)
REVERT: B  565 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8599 (pp20)
  outliers start: 19
  outliers final: 14
  residues processed: 104
  average time/residue: 0.2100
  time to fit residues: 27.8563
Evaluate side-chains
  106 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  445 TYR
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain B residue  565 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.173596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.142424 restraints weight = 22975.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 2.33
r_work: 0.3561 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.2915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6732  Z= 0.152
  Angle     :  0.482   5.482   9132  Z= 0.263
  Chirality :  0.035   0.133    987
  Planarity :  0.004   0.037   1093
  Dihedral  : 13.992 156.181   1027
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.75 %
    Favored  : 81.58 %
  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:  2.84 (0.30), residues: 750
  helix:  2.79 (0.20), residues: 593
  sheet:  None (None), residues: 0
  loop : -1.98 (0.38), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 472 
 TYR   0.015   0.001   TYR B 518 
 PHE   0.022   0.001   PHE A 605 
 TRP   0.012   0.002   TRP B 573 
 HIS   0.004   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 6730)
  covalent geometry    : angle       0.48197 ( 9128)
  SS BOND              : bond        0.00389 (    2)
  SS BOND              : angle       1.03614 (    4)
  hydrogen bonds       : bond        0.05196 (  468)
  hydrogen bonds       : angle       4.00261 ( 1404)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 TYR cc_start: 0.7421 (t80) cc_final: 0.6232 (m-10)
REVERT: A  468 ARG cc_start: 0.6670 (ttt180) cc_final: 0.6275 (ttm170)
REVERT: A  504 HIS cc_start: 0.6873 (OUTLIER) cc_final: 0.6501 (m-70)
REVERT: A  544 ASN cc_start: 0.7220 (OUTLIER) cc_final: 0.6886 (m-40)
REVERT: A  550 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6793 (mt-10)
REVERT: A  624 ARG cc_start: 0.7720 (mtm110) cc_final: 0.7295 (mtm-85)
REVERT: B  293 ARG cc_start: 0.7732 (mmm-85) cc_final: 0.6541 (ttm170)
REVERT: B  314 GLN cc_start: 0.5555 (mt0) cc_final: 0.4905 (mm-40)
REVERT: B  442 LYS cc_start: 0.8170 (tptm) cc_final: 0.7877 (mptt)
REVERT: B  565 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8626 (pp20)
  outliers start: 18
  outliers final: 14
  residues processed: 110
  average time/residue: 0.2284
  time to fit residues: 31.8718
Evaluate side-chains
  111 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  445 TYR
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  506 ASP
Chi-restraints excluded: chain A residue  544 ASN
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain B residue  565 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.171924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.140743 restraints weight = 22927.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 2.30
r_work: 0.3521 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.3245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6732  Z= 0.160
  Angle     :  0.496   5.361   9132  Z= 0.272
  Chirality :  0.036   0.134    987
  Planarity :  0.004   0.036   1093
  Dihedral  : 13.677 146.732   1027
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 15.16 %
    Favored  : 81.72 %
  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:  2.73 (0.30), residues: 750
  helix:  2.71 (0.20), residues: 593
  sheet:  None (None), residues: 0
  loop : -2.03 (0.38), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 371 
 TYR   0.016   0.002   TYR B 518 
 PHE   0.023   0.001   PHE A 605 
 TRP   0.012   0.001   TRP A 573 
 HIS   0.013   0.001   HIS A 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 6730)
  covalent geometry    : angle       0.49582 ( 9128)
  SS BOND              : bond        0.00412 (    2)
  SS BOND              : angle       1.06239 (    4)
  hydrogen bonds       : bond        0.05334 (  468)
  hydrogen bonds       : angle       4.04196 ( 1404)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 TYR cc_start: 0.7447 (t80) cc_final: 0.6206 (m-10)
REVERT: A  468 ARG cc_start: 0.6569 (ttt180) cc_final: 0.6261 (ttm170)
REVERT: A  504 HIS cc_start: 0.6900 (OUTLIER) cc_final: 0.6335 (m90)
REVERT: A  544 ASN cc_start: 0.7211 (OUTLIER) cc_final: 0.6914 (m-40)
REVERT: A  550 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6820 (mt-10)
REVERT: A  624 ARG cc_start: 0.7749 (mtm110) cc_final: 0.7362 (mtm-85)
REVERT: B  442 LYS cc_start: 0.8181 (tptm) cc_final: 0.7841 (mptt)
  outliers start: 21
  outliers final: 13
  residues processed: 105
  average time/residue: 0.2358
  time to fit residues: 31.6224
Evaluate side-chains
  105 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  506 ASP
Chi-restraints excluded: chain A residue  544 ASN
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  538 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 36 optimal weight:    0.3980
   chunk 15 optimal weight:    0.6980
   chunk 20 optimal weight:    0.1980
   chunk 13 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3976 r_free = 0.3976 target = 0.173271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.142671 restraints weight = 22834.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 2.30
r_work: 0.3516 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.3325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6732  Z= 0.129
  Angle     :  0.472   6.288   9132  Z= 0.259
  Chirality :  0.035   0.133    987
  Planarity :  0.004   0.045   1093
  Dihedral  : 13.192 136.723   1027
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 16.05 %
    Favored  : 81.43 %
  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:  2.91 (0.30), residues: 750
  helix:  2.86 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.01 (0.38), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 371 
 TYR   0.015   0.001   TYR B 518 
 PHE   0.019   0.001   PHE A 605 
 TRP   0.010   0.001   TRP A 573 
 HIS   0.008   0.001   HIS A 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6730)
  covalent geometry    : angle       0.47136 ( 9128)
  SS BOND              : bond        0.00412 (    2)
  SS BOND              : angle       1.10323 (    4)
  hydrogen bonds       : bond        0.05083 (  468)
  hydrogen bonds       : angle       3.95942 ( 1404)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 TYR cc_start: 0.7388 (t80) cc_final: 0.6155 (m-10)
REVERT: A  468 ARG cc_start: 0.6559 (ttt180) cc_final: 0.6234 (ttm170)
REVERT: A  471 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7596 (tppt)
REVERT: A  504 HIS cc_start: 0.7006 (OUTLIER) cc_final: 0.5994 (m90)
REVERT: A  544 ASN cc_start: 0.7277 (OUTLIER) cc_final: 0.7004 (m-40)
REVERT: A  550 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6837 (mt-10)
REVERT: A  624 ARG cc_start: 0.7773 (mtm110) cc_final: 0.7414 (mtm-85)
REVERT: B  314 GLN cc_start: 0.5761 (mt0) cc_final: 0.5293 (mm-40)
REVERT: B  388 LYS cc_start: 0.7552 (ptmt) cc_final: 0.7340 (ttpt)
REVERT: B  442 LYS cc_start: 0.8186 (tptm) cc_final: 0.7824 (mptt)
  outliers start: 17
  outliers final: 15
  residues processed: 108
  average time/residue: 0.2391
  time to fit residues: 32.8960
Evaluate side-chains
  113 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  505 SER
Chi-restraints excluded: chain A residue  544 ASN
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  248 ASN
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 38 optimal weight:    0.1980
   chunk 68 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.172280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.141623 restraints weight = 22770.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 2.29
r_work: 0.3519 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.3493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6732  Z= 0.143
  Angle     :  0.480   6.162   9132  Z= 0.263
  Chirality :  0.035   0.133    987
  Planarity :  0.004   0.036   1093
  Dihedral  : 12.687 113.784   1027
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.05 %
    Favored  : 81.58 %
  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:  2.84 (0.30), residues: 750
  helix:  2.80 (0.20), residues: 593
  sheet:  None (None), residues: 0
  loop : -2.03 (0.39), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 459 
 TYR   0.016   0.001   TYR B 518 
 PHE   0.027   0.001   PHE A 511 
 TRP   0.011   0.001   TRP A 573 
 HIS   0.008   0.001   HIS A 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6730)
  covalent geometry    : angle       0.47924 ( 9128)
  SS BOND              : bond        0.00396 (    2)
  SS BOND              : angle       1.09468 (    4)
  hydrogen bonds       : bond        0.05158 (  468)
  hydrogen bonds       : angle       3.97228 ( 1404)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 TYR cc_start: 0.7393 (t80) cc_final: 0.6162 (m-10)
REVERT: A  468 ARG cc_start: 0.6520 (ttt180) cc_final: 0.6210 (ttm170)
REVERT: A  471 LYS cc_start: 0.7964 (ttmm) cc_final: 0.7494 (mmtt)
REVERT: A  504 HIS cc_start: 0.7014 (OUTLIER) cc_final: 0.6096 (m90)
REVERT: A  544 ASN cc_start: 0.7313 (OUTLIER) cc_final: 0.7027 (m-40)
REVERT: A  550 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6860 (mt-10)
REVERT: A  624 ARG cc_start: 0.7816 (mtm110) cc_final: 0.7464 (mtm-85)
REVERT: B  314 GLN cc_start: 0.5840 (mt0) cc_final: 0.5384 (mm-40)
REVERT: B  442 LYS cc_start: 0.8178 (tptm) cc_final: 0.7810 (mptt)
  outliers start: 16
  outliers final: 14
  residues processed: 105
  average time/residue: 0.2365
  time to fit residues: 31.5303
Evaluate side-chains
  108 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  505 SER
Chi-restraints excluded: chain A residue  544 ASN
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 48 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.171164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.139903 restraints weight = 22989.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 2.24
r_work: 0.3491 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6732  Z= 0.150
  Angle     :  0.489   4.735   9132  Z= 0.268
  Chirality :  0.036   0.133    987
  Planarity :  0.004   0.037   1093
  Dihedral  : 12.136 102.876   1027
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 15.90 %
    Favored  : 81.28 %
  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: 750
  helix:  2.73 (0.20), residues: 593
  sheet:  None (None), residues: 0
  loop : -2.03 (0.40), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 273 
 TYR   0.017   0.001   TYR B 518 
 PHE   0.022   0.001   PHE A 605 
 TRP   0.011   0.001   TRP A 573 
 HIS   0.007   0.001   HIS A 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 6730)
  covalent geometry    : angle       0.48857 ( 9128)
  SS BOND              : bond        0.00422 (    2)
  SS BOND              : angle       1.12538 (    4)
  hydrogen bonds       : bond        0.05288 (  468)
  hydrogen bonds       : angle       4.01650 ( 1404)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 ARG cc_start: 0.6553 (ttt180) cc_final: 0.6262 (ttm170)
REVERT: A  471 LYS cc_start: 0.7957 (ttmm) cc_final: 0.7497 (mmtt)
REVERT: A  504 HIS cc_start: 0.7169 (OUTLIER) cc_final: 0.6239 (m90)
REVERT: A  544 ASN cc_start: 0.7344 (OUTLIER) cc_final: 0.7084 (m-40)
REVERT: A  550 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6929 (mt-10)
REVERT: A  624 ARG cc_start: 0.7845 (mtm110) cc_final: 0.7512 (mtm-85)
  outliers start: 19
  outliers final: 16
  residues processed: 103
  average time/residue: 0.2283
  time to fit residues: 29.7796
Evaluate side-chains
  109 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  445 TYR
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  505 SER
Chi-restraints excluded: chain A residue  506 ASP
Chi-restraints excluded: chain A residue  544 ASN
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  248 ASN
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  538 ASP
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0020
   chunk 61 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.6988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.171742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.140187 restraints weight = 23057.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.25
r_work: 0.3515 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.3812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6732  Z= 0.141
  Angle     :  0.475   4.719   9132  Z= 0.262
  Chirality :  0.035   0.134    987
  Planarity :  0.004   0.037   1093
  Dihedral  : 11.617 102.567   1027
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 15.45 %
    Favored  : 81.72 %
  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:  2.74 (0.30), residues: 750
  helix:  2.72 (0.20), residues: 593
  sheet:  None (None), residues: 0
  loop : -2.05 (0.40), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 624 
 TYR   0.016   0.001   TYR B 518 
 PHE   0.021   0.001   PHE A 605 
 TRP   0.010   0.001   TRP A 573 
 HIS   0.007   0.001   HIS A 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 6730)
  covalent geometry    : angle       0.47425 ( 9128)
  SS BOND              : bond        0.00453 (    2)
  SS BOND              : angle       1.21102 (    4)
  hydrogen bonds       : bond        0.05204 (  468)
  hydrogen bonds       : angle       4.00840 ( 1404)

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 ARG cc_start: 0.6516 (ttt180) cc_final: 0.6233 (ttm170)
REVERT: A  471 LYS cc_start: 0.7922 (ttmm) cc_final: 0.7480 (mmtt)
REVERT: A  504 HIS cc_start: 0.7120 (OUTLIER) cc_final: 0.6200 (m90)
REVERT: A  544 ASN cc_start: 0.7242 (OUTLIER) cc_final: 0.6965 (m-40)
REVERT: A  550 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7022 (mt-10)
REVERT: A  624 ARG cc_start: 0.7827 (mtm110) cc_final: 0.7506 (mtm-85)
REVERT: B  442 LYS cc_start: 0.8155 (tptm) cc_final: 0.7789 (mptt)
REVERT: B  615 GLU cc_start: 0.7407 (tp30) cc_final: 0.7110 (tp30)
  outliers start: 19
  outliers final: 16
  residues processed: 107
  average time/residue: 0.2354
  time to fit residues: 32.0071
Evaluate side-chains
  112 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 TYR
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  445 TYR
Chi-restraints excluded: chain A residue  504 HIS
Chi-restraints excluded: chain A residue  505 SER
Chi-restraints excluded: chain A residue  506 ASP
Chi-restraints excluded: chain A residue  544 ASN
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  620 CYS
Chi-restraints excluded: chain B residue  248 ASN
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  334 CYS
Chi-restraints excluded: chain B residue  367 TYR
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  454 ILE
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 43 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 44 optimal weight:    0.0770
   chunk 28 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.5138

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.172255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.141765 restraints weight = 22713.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 2.18
r_work: 0.3546 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.3828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6732  Z= 0.125
  Angle     :  0.462   5.157   9132  Z= 0.254
  Chirality :  0.035   0.133    987
  Planarity :  0.003   0.036   1093
  Dihedral  : 10.865  99.126   1027
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.60 %
    Favored  : 82.02 %
  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:  2.85 (0.30), residues: 750
  helix:  2.81 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.01 (0.39), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 371 
 TYR   0.015   0.001   TYR B 518 
 PHE   0.018   0.001   PHE A 605 
 TRP   0.011   0.001   TRP B 266 
 HIS   0.007   0.001   HIS A 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6730)
  covalent geometry    : angle       0.46145 ( 9128)
  SS BOND              : bond        0.00393 (    2)
  SS BOND              : angle       1.11564 (    4)
  hydrogen bonds       : bond        0.04997 (  468)
  hydrogen bonds       : angle       3.95214 ( 1404)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2994.81 seconds
wall clock time: 51 minutes 34.71 seconds (3094.71 seconds total)