Starting phenix.real_space_refine
on Wed Apr 30 11:23:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9biu_44602/04_2025/9biu_44602_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9biu_44602/04_2025/9biu_44602.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9biu_44602/04_2025/9biu_44602.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9biu_44602/04_2025/9biu_44602.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9biu_44602/04_2025/9biu_44602_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9biu_44602/04_2025/9biu_44602_trim.cif"
  }
  resolution = 2.9
  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=   0.036
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
     S      34      5.16       5
     Cl      1      4.86       5
     C    3105      2.51       5
     N     767      2.21       5
     O     813      1.98       5
     H    4738      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9458
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7539
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 472, 7529
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 21, 'TRANS': 450}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 472, 7529
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 21, 'TRANS': 450}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 7620
    Chain: "B"
      Number of atoms: 1890
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 1890
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 4, 'TRANS': 118}
    Chain: "A"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'CXN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 9.26, per 1000 atoms: 0.98
  Number of scatterers: 9458
  At special positions: 0
  Unit cell: (86.376, 110.532, 83.448, 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)
     Cl      1     17.00
     S      34     16.00
     O     813      8.00
     N     767      7.00
     C    3105      6.00
     H    4738      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS A 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " 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: 2.97
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1106

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 2 sheets defined
      63.4% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 45
      No H-bonds generated for 'chain 'A' and resid 43 through 45'
    Processing helix  chain 'A' and resid 46 through 74
      removed outlier: 5.003A  pdb=" N   ASN A  52 " --> pdb=" O   PHE A  48 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   VAL A  66 " --> pdb=" O   GLY A  62 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   THR A  68 " --> pdb=" O   LYS A  64 " (cutoff:3.500A)
      removed outlier: 4.976A  pdb=" N   LEU A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 107
      Proline residue:  A  97  - end of helix
    Processing helix  chain 'A' and resid 112 through 131
    Processing helix  chain 'A' and resid 140 through 170
      removed outlier: 4.192A  pdb=" N   GLY A 159 " --> pdb=" O   LEU A 155 " (cutoff:3.500A)
      Proline residue:  A 162  - end of helix
      removed outlier: 3.697A  pdb=" N   ALA A 165 " --> pdb=" O   LYS A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 206
      removed outlier: 3.584A  pdb=" N   ARG A 180 " --> pdb=" O   HIS A 176 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   THR A 181 " --> pdb=" O   ALA A 177 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ARG A 182 " --> pdb=" O   GLU A 178 " (cutoff:3.500A)
      Proline residue:  A 203  - end of helix
      removed outlier: 3.615A  pdb=" N   ARG A 206 " --> pdb=" O   THR A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 238
      removed outlier: 3.990A  pdb=" N   ALA A 220 " --> pdb=" O   CYS A 216 " (cutoff:3.500A)
      Proline residue:  A 224  - end of helix
      removed outlier: 3.767A  pdb=" N   GLY A 238 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 242
    Processing helix  chain 'A' and resid 250 through 266
      removed outlier: 3.845A  pdb=" N   ARG A 266 " --> pdb=" O   ALA A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 307
      removed outlier: 3.826A  pdb=" N   ASP A 295 " --> pdb=" O   HIS A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 318
      removed outlier: 3.645A  pdb=" N   PHE A 312 " --> pdb=" O   PRO A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 329
      removed outlier: 3.525A  pdb=" N   LEU A 325 " --> pdb=" O   SER A 321 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS A 329 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 345
    Processing helix  chain 'A' and resid 346 through 362
      removed outlier: 3.587A  pdb=" N   PHE A 350 " --> pdb=" O   VAL A 346 " (cutoff:3.500A)
      Proline residue:  A 357  - end of helix
    Processing helix  chain 'A' and resid 362 through 370
      removed outlier: 3.800A  pdb=" N   CYS A 370 " --> pdb=" O   LEU A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 403
    Processing helix  chain 'A' and resid 611 through 636
      removed outlier: 3.660A  pdb=" N   THR A 628 " --> pdb=" O   MET A 624 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLU A 631 " --> pdb=" O   VAL A 627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 638 through 640
      No H-bonds generated for 'chain 'A' and resid 638 through 640'
    Processing helix  chain 'A' and resid 641 through 665
      removed outlier: 3.548A  pdb=" N   LEU A 645 " --> pdb=" O   MET A 641 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN A 646 " --> pdb=" O   LYS A 642 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL A 653 " --> pdb=" O   TRP A 649 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   GLN A 665 " --> pdb=" O   LEU A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 695
    Processing helix  chain 'B' and resid 28 through 30
      No H-bonds generated for 'chain 'B' and resid 28 through 30'
    Processing helix  chain 'B' and resid 53 through 56
      removed outlier: 4.270A  pdb=" N   ARG B  56 " --> pdb=" O   TRP B  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 53 through 56'
    Processing helix  chain 'B' and resid 110 through 114
    Processing sheet with id=AA1, first strand: chain 'B' and resid 18 through 23
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 60
      removed outlier: 6.621A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   SER B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   MET B  34 " --> pdb=" O   SER B  50 " (cutoff:3.500A)

    276 hydrogen bonds defined for protein.
    797 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: 4.10

  Time building geometry restraints manager: 3.36 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 4729
        1.04 -     1.24: 637
        1.24 -     1.44: 1486
        1.44 -     1.64: 2681
        1.64 -     1.84: 55
  Bond restraints: 9588
  Sorted by residual:
  bond pdb=" N25 CXN A 801 "
       pdb=" O24 CXN A 801 "
    ideal  model  delta    sigma   weight residual
    1.363  1.418 -0.055 2.00e-02 2.50e+03 7.45e+00
  bond pdb=" N   VAL B  87 "
       pdb=" H   VAL B  87 "
    ideal  model  delta    sigma   weight residual
    0.860  0.913 -0.053 2.00e-02 2.50e+03 6.93e+00
  bond pdb=" N   VAL B  87 "
       pdb=" CA  VAL B  87 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.029 1.23e-02 6.61e+03 5.39e+00
  bond pdb=" C6  CXN A 801 "
       pdb=" C8  CXN A 801 "
    ideal  model  delta    sigma   weight residual
    1.546  1.510  0.036 2.00e-02 2.50e+03 3.26e+00
  bond pdb=" C2  CXN A 801 "
       pdb=" N2  CXN A 801 "
    ideal  model  delta    sigma   weight residual
    1.421  1.455 -0.034 2.00e-02 2.50e+03 2.94e+00
  ... (remaining 9583 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 17041
        1.59 -     3.19: 248
        3.19 -     4.78: 26
        4.78 -     6.38: 1
        6.38 -     7.97: 2
  Bond angle restraints: 17318
  Sorted by residual:
  angle pdb=" CA  GLN A 278 "
        pdb=" CB  GLN A 278 "
        pdb=" CG  GLN A 278 "
      ideal   model   delta    sigma   weight residual
     114.10  122.07   -7.97 2.00e+00 2.50e-01 1.59e+01
  angle pdb=" N   PRO B  88 "
        pdb=" CA  PRO B  88 "
        pdb=" C   PRO B  88 "
      ideal   model   delta    sigma   weight residual
     113.75  109.70    4.05 1.49e+00 4.50e-01 7.38e+00
  angle pdb=" N   ASP A 273 "
        pdb=" CA  ASP A 273 "
        pdb=" C   ASP A 273 "
      ideal   model   delta    sigma   weight residual
     113.18  109.62    3.56 1.33e+00 5.65e-01 7.18e+00
  angle pdb=" N   GLN A 278 "
        pdb=" CA  GLN A 278 "
        pdb=" C   GLN A 278 "
      ideal   model   delta    sigma   weight residual
     113.28  109.19    4.09 1.57e+00 4.06e-01 6.80e+00
  angle pdb=" N   THR A  96 "
        pdb=" CA  THR A  96 "
        pdb=" C   THR A  96 "
      ideal   model   delta    sigma   weight residual
     109.81  115.30   -5.49 2.21e+00 2.05e-01 6.18e+00
  ... (remaining 17313 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.61: 3974
       17.61 -    35.22: 391
       35.22 -    52.82: 140
       52.82 -    70.43: 40
       70.43 -    88.04: 4
  Dihedral angle restraints: 4549
    sinusoidal: 2406
      harmonic: 2143
  Sorted by residual:
  dihedral pdb=" CA  TRP A 283 "
           pdb=" C   TRP A 283 "
           pdb=" N   ALA A 284 "
           pdb=" CA  ALA A 284 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.17   23.83     0      5.00e+00 4.00e-02 2.27e+01
  dihedral pdb=" CA  GLY A 159 "
           pdb=" C   GLY A 159 "
           pdb=" N   ILE A 160 "
           pdb=" CA  ILE A 160 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.47   20.53     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  LYS A 110 "
           pdb=" C   LYS A 110 "
           pdb=" N   PHE A 111 "
           pdb=" CA  PHE A 111 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.37  -19.63     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 4546 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 619
       0.047 -    0.094: 98
       0.094 -    0.142: 20
       0.142 -    0.189: 1
       0.189 -    0.236: 1
  Chirality restraints: 739
  Sorted by residual:
  chirality pdb=" CA  VAL B  87 "
            pdb=" N   VAL B  87 "
            pdb=" C   VAL B  87 "
            pdb=" CB  VAL B  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  ILE A  49 "
            pdb=" N   ILE A  49 "
            pdb=" C   ILE A  49 "
            pdb=" CB  ILE A  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.65e-01
  chirality pdb=" CA  ILE A 133 "
            pdb=" N   ILE A 133 "
            pdb=" C   ILE A 133 "
            pdb=" CB  ILE A 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.59e-01
  ... (remaining 736 not shown)

  Planarity restraints: 1384
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C26 CXN A 801 "   -0.036 2.00e-02 2.50e+03   1.94e-02 7.54e+00
        pdb=" C28 CXN A 801 "    0.022 2.00e-02 2.50e+03
        pdb=" C29 CXN A 801 "    0.006 2.00e-02 2.50e+03
        pdb=" C30 CXN A 801 "   -0.015 2.00e-02 2.50e+03
        pdb=" C31 CXN A 801 "   -0.016 2.00e-02 2.50e+03
        pdb=" C32 CXN A 801 "    0.002 2.00e-02 2.50e+03
        pdb=" C33 CXN A 801 "    0.023 2.00e-02 2.50e+03
        pdb="CL   CXN A 801 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 278 "    0.011 2.00e-02 2.50e+03   2.13e-02 4.55e+00
        pdb=" C   GLN A 278 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   GLN A 278 "    0.014 2.00e-02 2.50e+03
        pdb=" N   HIS A 279 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 307 "   -0.035 5.00e-02 4.00e+02   5.25e-02 4.42e+00
        pdb=" N   PRO A 308 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 308 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 308 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1381 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 910
        2.23 -     2.82: 20649
        2.82 -     3.42: 24921
        3.42 -     4.01: 34102
        4.01 -     4.60: 52430
  Nonbonded interactions: 133012
  Sorted by model distance:
  nonbonded pdb=" O   TRP B  53 "
            pdb=" HG  SER B  54 "
     model   vdw
     1.639 2.450
  nonbonded pdb=" O   HIS A  76 "
            pdb=" H   THR B 108 "
     model   vdw
     1.680 2.450
  nonbonded pdb=" OD1 ASP A 170 "
            pdb=" HH  TYR A 634 "
     model   vdw
     1.695 2.450
  nonbonded pdb=" HE  ARG B  45 "
            pdb=" OE2 GLU B 111 "
     model   vdw
     1.700 2.450
  nonbonded pdb=" O   ARG A 266 "
            pdb=" H   ARG A 268 "
     model   vdw
     1.703 2.450
  ... (remaining 133007 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.38 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:             7.240
  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:             0.170
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     29.940
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:15.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
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      :  0.003   0.055   4851  Z= 0.133
  Angle     :  0.563   7.969   6598  Z= 0.302
  Chirality :  0.037   0.236    739
  Planarity :  0.004   0.053    816
  Dihedral  : 17.103  88.040   1730
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 23.95 %
    Favored  : 74.05 %
  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:  0.77 (0.36), residues: 590
  helix:  1.97 (0.29), residues: 341
  sheet: -0.96 (0.72), residues: 59
  loop : -1.79 (0.41), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 279 
 PHE   0.009   0.001   PHE A  48 
 TYR   0.008   0.001   TYR A 183 
 ARG   0.002   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14813 (  276)
  hydrogen bonds       : angle       5.30956 (  797)
  SS BOND              : bond        0.00021 (    2)
  SS BOND              : angle       1.45494 (    4)
  covalent geometry    : bond        0.00271 ( 4849)
  covalent geometry    : angle       0.56154 ( 6594)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 8
  residues processed: 77
  average time/residue: 1.8829
  time to fit residues: 153.4667
Evaluate side-chains
  74 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   59 SER
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain B residue   25 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0030
   chunk 46 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0770
   chunk 28 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.4748

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.165959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.133035 restraints weight = 22004.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3794 rms_B_bonded: 2.53
r_work: 0.3633 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3487 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3517
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3517
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.0505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4851  Z= 0.138
  Angle     :  0.565   7.064   6598  Z= 0.298
  Chirality :  0.038   0.149    739
  Planarity :  0.004   0.050    816
  Dihedral  :  7.295  57.403    691
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 22.16 %
    Favored  : 74.45 %
  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:  0.73 (0.35), residues: 590
  helix:  1.98 (0.28), residues: 339
  sheet: -1.12 (0.70), residues: 59
  loop : -1.80 (0.41), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 291 
 PHE   0.018   0.001   PHE A  48 
 TYR   0.013   0.001   TYR A 634 
 ARG   0.002   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04941 (  276)
  hydrogen bonds       : angle       4.23315 (  797)
  SS BOND              : bond        0.00196 (    2)
  SS BOND              : angle       1.59073 (    4)
  covalent geometry    : bond        0.00307 ( 4849)
  covalent geometry    : angle       0.56395 ( 6594)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.8130 (p)
REVERT: A  374 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8130 (m-10)
REVERT: B   56 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7608 (mtp180)
REVERT: B  119 GLN cc_start: 0.7003 (mp10) cc_final: 0.6703 (mp10)
  outliers start: 17
  outliers final: 6
  residues processed: 78
  average time/residue: 2.0890
  time to fit residues: 172.4164
Evaluate side-chains
  76 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  104 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 25 optimal weight:    0.2980
   chunk 10 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 11 optimal weight:    0.4980
   chunk 52 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.164761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.132117 restraints weight = 19345.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 2.41
r_work: 0.3604 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3461 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3505
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3505 r_free = 0.3505    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3505 r_free = 0.3505    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3505
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.0754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4851  Z= 0.163
  Angle     :  0.572   6.970   6598  Z= 0.302
  Chirality :  0.039   0.149    739
  Planarity :  0.004   0.049    816
  Dihedral  :  7.027  57.640    687
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 22.95 %
    Favored  : 73.85 %
  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:  0.56 (0.35), residues: 590
  helix:  1.88 (0.28), residues: 339
  sheet: -1.32 (0.68), residues: 59
  loop : -1.88 (0.41), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 291 
 PHE   0.022   0.001   PHE A  48 
 TYR   0.012   0.001   TYR A 634 
 ARG   0.002   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04679 (  276)
  hydrogen bonds       : angle       4.14938 (  797)
  SS BOND              : bond        0.00209 (    2)
  SS BOND              : angle       1.69537 (    4)
  covalent geometry    : bond        0.00382 ( 4849)
  covalent geometry    : angle       0.57065 ( 6594)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.706 
Fit side-chains
REVERT: A   99 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7609 (tt)
REVERT: A  198 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.8140 (p)
REVERT: A  212 PHE cc_start: 0.7415 (m-80) cc_final: 0.7124 (m-80)
REVERT: A  374 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8114 (m-10)
REVERT: B   31 ASP cc_start: 0.8157 (t0) cc_final: 0.7892 (t0)
REVERT: B   56 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7609 (mtp180)
REVERT: B  106 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7932 (ptpt)
  outliers start: 16
  outliers final: 5
  residues processed: 75
  average time/residue: 1.7973
  time to fit residues: 142.4365
Evaluate side-chains
  73 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain A residue  376 SER
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  106 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0040
   chunk 31 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.6992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.163801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.131337 restraints weight = 20032.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 2.42
r_work: 0.3595 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3457 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3497
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3497 r_free = 0.3497    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3497 r_free = 0.3497    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3497
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.0888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4851  Z= 0.165
  Angle     :  0.572   6.896   6598  Z= 0.301
  Chirality :  0.039   0.150    739
  Planarity :  0.004   0.049    816
  Dihedral  :  6.915  58.983    686
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 23.35 %
    Favored  : 73.65 %
  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:  0.51 (0.35), residues: 590
  helix:  1.80 (0.28), residues: 341
  sheet: -1.46 (0.67), residues: 59
  loop : -1.82 (0.41), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 279 
 PHE   0.022   0.001   PHE A  48 
 TYR   0.012   0.001   TYR A 634 
 ARG   0.002   0.000   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04502 (  276)
  hydrogen bonds       : angle       4.08962 (  797)
  SS BOND              : bond        0.00235 (    2)
  SS BOND              : angle       1.66306 (    4)
  covalent geometry    : bond        0.00386 ( 4849)
  covalent geometry    : angle       0.57088 ( 6594)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.8135 (p)
REVERT: A  278 GLN cc_start: 0.7575 (tp40) cc_final: 0.7325 (tp40)
REVERT: A  374 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.8123 (m-10)
REVERT: B   56 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7650 (mtp180)
REVERT: B  106 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8037 (ptpt)
  outliers start: 15
  outliers final: 4
  residues processed: 75
  average time/residue: 2.3425
  time to fit residues: 184.3963
Evaluate side-chains
  70 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 1.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  106 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 57 optimal weight:    0.0050
   chunk 56 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 39 optimal weight:    0.4980
   chunk 10 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0970
   chunk 32 optimal weight:    0.2980
   chunk 15 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.3192

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.167117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.135569 restraints weight = 16599.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3813 rms_B_bonded: 2.21
r_work: 0.3642 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3502 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3541
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3541 r_free = 0.3541    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3541 r_free = 0.3541    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3541
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.0969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4851  Z= 0.115
  Angle     :  0.539   6.662   6598  Z= 0.284
  Chirality :  0.037   0.148    739
  Planarity :  0.004   0.048    816
  Dihedral  :  6.548  58.120    685
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 23.55 %
    Favored  : 73.65 %
  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:  0.68 (0.35), residues: 590
  helix:  2.01 (0.28), residues: 340
  sheet: -1.37 (0.68), residues: 59
  loop : -1.88 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 279 
 PHE   0.017   0.001   PHE A  48 
 TYR   0.010   0.001   TYR A 634 
 ARG   0.002   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03963 (  276)
  hydrogen bonds       : angle       3.96533 (  797)
  SS BOND              : bond        0.00085 (    2)
  SS BOND              : angle       1.55926 (    4)
  covalent geometry    : bond        0.00253 ( 4849)
  covalent geometry    : angle       0.53742 ( 6594)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.649 
Fit side-chains
REVERT: A  198 SER cc_start: 0.8457 (OUTLIER) cc_final: 0.8144 (p)
REVERT: A  278 GLN cc_start: 0.7607 (tp40) cc_final: 0.7333 (tp40)
REVERT: B   31 ASP cc_start: 0.8064 (t0) cc_final: 0.7717 (t0)
REVERT: B   56 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7675 (mtp180)
  outliers start: 14
  outliers final: 5
  residues processed: 74
  average time/residue: 2.0556
  time to fit residues: 159.6564
Evaluate side-chains
  69 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  104 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 57 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.164688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.131726 restraints weight = 19097.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 2.41
r_work: 0.3602 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3465 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3504
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3504 r_free = 0.3504    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3504 r_free = 0.3504    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3504
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4851  Z= 0.172
  Angle     :  0.571   6.813   6598  Z= 0.303
  Chirality :  0.039   0.149    739
  Planarity :  0.005   0.050    816
  Dihedral  :  6.654  56.162    685
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 23.95 %
    Favored  : 73.45 %
  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:  0.56 (0.35), residues: 590
  helix:  1.88 (0.28), residues: 340
  sheet: -1.41 (0.68), residues: 59
  loop : -1.88 (0.40), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 279 
 PHE   0.023   0.001   PHE A  48 
 TYR   0.013   0.001   TYR A 634 
 ARG   0.002   0.000   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04452 (  276)
  hydrogen bonds       : angle       4.02363 (  797)
  SS BOND              : bond        0.00261 (    2)
  SS BOND              : angle       1.66866 (    4)
  covalent geometry    : bond        0.00405 ( 4849)
  covalent geometry    : angle       0.56950 ( 6594)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7620 (tt)
REVERT: A  198 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.8124 (p)
REVERT: A  266 ARG cc_start: 0.7517 (mtm180) cc_final: 0.7226 (mtm-85)
REVERT: A  278 GLN cc_start: 0.7641 (tp40) cc_final: 0.7376 (tp40)
REVERT: A  374 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8148 (m-10)
REVERT: B   31 ASP cc_start: 0.8096 (t0) cc_final: 0.7745 (t0)
REVERT: B   56 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7676 (mtp180)
REVERT: B   67 ARG cc_start: 0.7771 (mmt-90) cc_final: 0.7486 (mmm160)
  outliers start: 13
  outliers final: 5
  residues processed: 76
  average time/residue: 2.7228
  time to fit residues: 216.6767
Evaluate side-chains
  74 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  104 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 9 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 3 optimal weight:    0.3980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.164606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.132398 restraints weight = 17487.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 2.29
r_work: 0.3617 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3475 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3513
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3513
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4851  Z= 0.165
  Angle     :  0.574   6.786   6598  Z= 0.303
  Chirality :  0.039   0.150    739
  Planarity :  0.005   0.050    816
  Dihedral  :  6.186  42.792    681
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 24.55 %
    Favored  : 72.65 %
  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:  0.56 (0.35), residues: 590
  helix:  1.86 (0.28), residues: 340
  sheet: -1.43 (0.68), residues: 59
  loop : -1.83 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 107 
 HIS   0.004   0.001   HIS A 279 
 PHE   0.022   0.001   PHE A  48 
 TYR   0.011   0.001   TYR A 634 
 ARG   0.002   0.000   ARG A 266 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04409 (  276)
  hydrogen bonds       : angle       4.02088 (  797)
  SS BOND              : bond        0.00208 (    2)
  SS BOND              : angle       1.69936 (    4)
  covalent geometry    : bond        0.00387 ( 4849)
  covalent geometry    : angle       0.57226 ( 6594)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7597 (tt)
REVERT: A  198 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.8098 (p)
REVERT: A  211 CYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6993 (m)
REVERT: A  278 GLN cc_start: 0.7662 (tp40) cc_final: 0.7338 (tp40)
REVERT: A  374 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8132 (m-10)
REVERT: B   31 ASP cc_start: 0.8092 (t0) cc_final: 0.7760 (t0)
REVERT: B   56 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7660 (mtp180)
REVERT: B   67 ARG cc_start: 0.7755 (mmt-90) cc_final: 0.7474 (mmm160)
REVERT: B  106 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7975 (ptpt)
  outliers start: 14
  outliers final: 6
  residues processed: 75
  average time/residue: 2.2711
  time to fit residues: 178.1895
Evaluate side-chains
  74 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  106 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 54 optimal weight:    0.2980
   chunk 23 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 26 optimal weight:    0.4980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.164341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.133066 restraints weight = 16199.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 2.17
r_work: 0.3612 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3513
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3513
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.1306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4851  Z= 0.163
  Angle     :  0.572   6.767   6598  Z= 0.303
  Chirality :  0.039   0.150    739
  Planarity :  0.005   0.050    816
  Dihedral  :  6.188  42.661    681
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 24.15 %
    Favored  : 73.05 %
  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:  0.58 (0.35), residues: 590
  helix:  1.87 (0.28), residues: 340
  sheet: -1.44 (0.68), residues: 59
  loop : -1.80 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 279 
 PHE   0.022   0.001   PHE A  48 
 TYR   0.012   0.001   TYR A 634 
 ARG   0.002   0.000   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04396 (  276)
  hydrogen bonds       : angle       4.00950 (  797)
  SS BOND              : bond        0.00200 (    2)
  SS BOND              : angle       1.66469 (    4)
  covalent geometry    : bond        0.00384 ( 4849)
  covalent geometry    : angle       0.57097 ( 6594)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7622 (tt)
REVERT: A  198 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8111 (p)
REVERT: A  211 CYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6977 (m)
REVERT: A  212 PHE cc_start: 0.7377 (OUTLIER) cc_final: 0.7089 (m-80)
REVERT: A  278 GLN cc_start: 0.7695 (tp40) cc_final: 0.7375 (tp40)
REVERT: A  374 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.8107 (m-10)
REVERT: B   31 ASP cc_start: 0.8099 (t0) cc_final: 0.7789 (t0)
REVERT: B   56 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7667 (mtp180)
REVERT: B  106 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8008 (ptpt)
  outliers start: 14
  outliers final: 6
  residues processed: 76
  average time/residue: 2.3492
  time to fit residues: 186.4317
Evaluate side-chains
  76 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain A residue  374 PHE
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  106 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 46 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0570
   chunk 43 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.4898

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.166832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.133724 restraints weight = 19101.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3778 rms_B_bonded: 2.42
r_work: 0.3627 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3488 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3519
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3519
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4851  Z= 0.135
  Angle     :  0.556   6.658   6598  Z= 0.294
  Chirality :  0.038   0.148    739
  Planarity :  0.004   0.050    816
  Dihedral  :  6.058  42.844    681
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 23.95 %
    Favored  : 73.25 %
  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:  0.69 (0.35), residues: 590
  helix:  1.96 (0.28), residues: 340
  sheet: -1.34 (0.69), residues: 59
  loop : -1.79 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 279 
 PHE   0.019   0.001   PHE A  48 
 TYR   0.011   0.001   TYR A 634 
 ARG   0.001   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04100 (  276)
  hydrogen bonds       : angle       3.93761 (  797)
  SS BOND              : bond        0.00136 (    2)
  SS BOND              : angle       1.56480 (    4)
  covalent geometry    : bond        0.00312 ( 4849)
  covalent geometry    : angle       0.55491 ( 6594)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7624 (tt)
REVERT: A  198 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.8118 (p)
REVERT: A  211 CYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6933 (m)
REVERT: A  278 GLN cc_start: 0.7710 (tp40) cc_final: 0.7403 (tp40)
REVERT: B   31 ASP cc_start: 0.8094 (t0) cc_final: 0.7817 (t0)
REVERT: B   56 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7716 (mtp180)
REVERT: B  115 GLU cc_start: 0.8464 (pt0) cc_final: 0.7960 (mp0)
  outliers start: 14
  outliers final: 5
  residues processed: 78
  average time/residue: 2.3239
  time to fit residues: 189.5762
Evaluate side-chains
  76 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain B residue   46 GLU
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  104 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0770
   chunk 13 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0980
   chunk 2 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0980
   overall best weight:    0.3338

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.167125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.134030 restraints weight = 19868.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 2.47
r_work: 0.3641 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3496 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3536
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3536 r_free = 0.3536    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3536 r_free = 0.3536    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3536
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.1331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4851  Z= 0.117
  Angle     :  0.541   6.565   6598  Z= 0.286
  Chirality :  0.037   0.147    739
  Planarity :  0.004   0.049    816
  Dihedral  :  5.698  42.837    678
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 24.75 %
    Favored  : 73.25 %
  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:  0.87 (0.35), residues: 590
  helix:  2.14 (0.28), residues: 334
  sheet: -1.29 (0.69), residues: 59
  loop : -1.63 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 279 
 PHE   0.016   0.001   PHE A  48 
 TYR   0.010   0.001   TYR A 634 
 ARG   0.001   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03832 (  276)
  hydrogen bonds       : angle       3.86672 (  797)
  SS BOND              : bond        0.00095 (    2)
  SS BOND              : angle       1.52471 (    4)
  covalent geometry    : bond        0.00263 ( 4849)
  covalent geometry    : angle       0.53967 ( 6594)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 SER cc_start: 0.8428 (OUTLIER) cc_final: 0.8096 (p)
REVERT: A  278 GLN cc_start: 0.7801 (tp40) cc_final: 0.7452 (tp40)
REVERT: B   31 ASP cc_start: 0.8049 (t0) cc_final: 0.7809 (t0)
REVERT: B   56 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7708 (mtp180)
REVERT: B  115 GLU cc_start: 0.8463 (pt0) cc_final: 0.7921 (mp0)
  outliers start: 10
  outliers final: 5
  residues processed: 74
  average time/residue: 2.1694
  time to fit residues: 168.6549
Evaluate side-chains
  73 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  212 PHE
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain B residue   56 ARG
Chi-restraints excluded: chain B residue  104 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 30 optimal weight:    0.3980
   chunk 14 optimal weight:    0.9990
   chunk 54 optimal weight:    0.3980
   chunk 21 optimal weight:    0.6980
   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 345 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.165122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.131986 restraints weight = 19934.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 2.47
r_work: 0.3605 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3464 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3505
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3505 r_free = 0.3505    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3505 r_free = 0.3505    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3505
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4851  Z= 0.155
  Angle     :  0.564   6.689   6598  Z= 0.299
  Chirality :  0.038   0.150    739
  Planarity :  0.004   0.050    816
  Dihedral  :  5.851  42.624    678
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 25.15 %
    Favored  : 73.25 %
  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:  0.73 (0.35), residues: 590
  helix:  2.00 (0.28), residues: 334
  sheet: -1.35 (0.69), residues: 59
  loop : -1.65 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 279 
 PHE   0.021   0.001   PHE A  48 
 TYR   0.013   0.001   TYR A 634 
 ARG   0.002   0.000   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04248 (  276)
  hydrogen bonds       : angle       3.92237 (  797)
  SS BOND              : bond        0.00211 (    2)
  SS BOND              : angle       1.61147 (    4)
  covalent geometry    : bond        0.00365 ( 4849)
  covalent geometry    : angle       0.56311 ( 6594)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9489.78 seconds
wall clock time: 166 minutes 21.49 seconds (9981.49 seconds total)