Starting phenix.real_space_refine
on Fri Mar 14 02:41:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9biu_44602/03_2025/9biu_44602_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9biu_44602/03_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_44602/03_2025/9biu_44602.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9biu_44602/03_2025/9biu_44602.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9biu_44602/03_2025/9biu_44602_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9biu_44602/03_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 9.17, per 1000 atoms: 0.97
  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: 2.57
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.68
  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: 3.46

  Time building geometry restraints manager: 3.02 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:             7.010
  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:             0.150
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     28.290
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:12.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.040
-------------------------------------------------------------------------------
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   4849  Z= 0.170
  Angle     :  0.562   7.969   6594  Z= 0.301
  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 

*********************** 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  : 0.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 8
  residues processed: 77
  average time/residue: 2.1607
  time to fit residues: 176.6837
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  : 0.989 
-------------------------------------------------------------------------------
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:    1.9990
   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:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.6590

-------------------------------------------------------------------------------
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 = 0.4130 r_free = 0.4130 target = 0.164899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.131700 restraints weight = 22000.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3761 rms_B_bonded: 2.54
r_work: 0.3587 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3625 r_free = 0.3625    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3625 r_free = 0.3625    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.0571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4849  Z= 0.238
  Angle     :  0.582   7.136   6594  Z= 0.308
  Chirality :  0.039   0.149    739
  Planarity :  0.004   0.051    816
  Dihedral  :  7.415  57.080    691
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 22.16 %
    Favored  : 74.25 %
  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:  0.61 (0.35), residues: 590
  helix:  1.88 (0.28), residues: 339
  sheet: -1.17 (0.69), residues: 59
  loop : -1.83 (0.41), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 291 
 PHE   0.022   0.002   PHE A  48 
 TYR   0.015   0.001   TYR A 634 
 ARG   0.002   0.000   ARG B  38 

*********************** 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
  87 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 SER cc_start: 0.8465 (OUTLIER) cc_final: 0.8122 (p)
REVERT: A  374 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.8064 (m-10)
REVERT: B   56 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7539 (mtp180)
REVERT: B  106 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7606 (ptpt)
  outliers start: 18
  outliers final: 6
  residues processed: 79
  average time/residue: 1.8329
  time to fit residues: 154.0604
Evaluate side-chains
  77 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain B residue  106 LYS
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:    0.0770
   chunk 10 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 13 optimal weight:    0.2980
   chunk 29 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.6538

-------------------------------------------------------------------------------
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 = 0.164616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.132140 restraints weight = 19327.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3756 rms_B_bonded: 2.40
r_work: 0.3602 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3468 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3508
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3508 r_free = 0.3508    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 = 0.3508 r_free = 0.3508    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3508
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.0788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4849  Z= 0.229
  Angle     :  0.568   6.953   6594  Z= 0.299
  Chirality :  0.039   0.149    739
  Planarity :  0.004   0.050    816
  Dihedral  :  7.061  57.162    687
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  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:  0.55 (0.35), residues: 590
  helix:  1.85 (0.28), residues: 339
  sheet: -1.31 (0.69), residues: 59
  loop : -1.86 (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 279 
 PHE   0.021   0.001   PHE A  48 
 TYR   0.011   0.001   TYR A 634 
 ARG   0.003   0.000   ARG B  38 

*********************** 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
  81 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.741 
Fit side-chains
REVERT: A   99 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7622 (tt)
REVERT: A  198 SER cc_start: 0.8458 (OUTLIER) cc_final: 0.8155 (p)
REVERT: A  212 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.7141 (m-80)
REVERT: A  374 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.8117 (m-10)
REVERT: B   56 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7625 (mtp180)
REVERT: B  106 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7812 (ptpt)
  outliers start: 16
  outliers final: 5
  residues processed: 75
  average time/residue: 1.9335
  time to fit residues: 153.2442
Evaluate side-chains
  74 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    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  198 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  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:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0980
   chunk 56 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 = 0.4117 r_free = 0.4117 target = 0.163700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.130983 restraints weight = 19941.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 2.42
r_work: 0.3585 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3436 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3484
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3484 r_free = 0.3484    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3484 r_free = 0.3484    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3484
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.0914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4849  Z= 0.261
  Angle     :  0.585   6.998   6594  Z= 0.309
  Chirality :  0.039   0.151    739
  Planarity :  0.005   0.051    816
  Dihedral  :  6.997  58.264    686
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 23.35 %
    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:  0.41 (0.35), residues: 590
  helix:  1.68 (0.28), residues: 344
  sheet: -1.48 (0.67), residues: 59
  loop : -1.84 (0.41), residues: 187

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   0.024   0.002   PHE A  48 
 TYR   0.012   0.001   TYR A 634 
 ARG   0.003   0.000   ARG B 102 

*********************** 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: 16
    poor density    : 63
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7660 (tt)
REVERT: A  198 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.8172 (p)
REVERT: A  374 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8151 (m-10)
REVERT: B   56 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7646 (mtp180)
REVERT: B  106 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7810 (ptpt)
  outliers start: 16
  outliers final: 6
  residues processed: 76
  average time/residue: 2.2415
  time to fit residues: 178.9957
Evaluate side-chains
  74 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  198 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  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:    0.0770
   chunk 56 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 39 optimal weight:    0.1980
   chunk 10 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0870
   chunk 32 optimal weight:    0.3980
   chunk 15 optimal weight:    0.1980
   chunk 34 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.1916

-------------------------------------------------------------------------------
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 = 0.4163 r_free = 0.4163 target = 0.168134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.136528 restraints weight = 16640.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 2.24
r_work: 0.3672 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3530 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3572
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3572 r_free = 0.3572    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3572 r_free = 0.3572    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3572
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4849  Z= 0.138
  Angle     :  0.534   6.710   6594  Z= 0.281
  Chirality :  0.037   0.146    739
  Planarity :  0.004   0.049    816
  Dihedral  :  6.465  58.201    685
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 23.55 %
    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:  0.74 (0.36), residues: 590
  helix:  2.06 (0.28), residues: 340
  sheet: -1.29 (0.69), residues: 59
  loop : -1.90 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 291 
 PHE   0.014   0.001   PHE A  48 
 TYR   0.008   0.001   TYR A 634 
 ARG   0.003   0.000   ARG B  38 

*********************** 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
  79 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 SER cc_start: 0.8418 (OUTLIER) cc_final: 0.8120 (p)
REVERT: B   31 ASP cc_start: 0.8102 (t0) cc_final: 0.7889 (t0)
REVERT: B  106 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7575 (ptpt)
REVERT: B  115 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7888 (pt0)
  outliers start: 15
  outliers final: 5
  residues processed: 75
  average time/residue: 2.0766
  time to fit residues: 163.5296
Evaluate side-chains
  68 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
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  212 PHE
Chi-restraints excluded: chain A residue  214 GLN
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  106 LYS
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:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.9780

-------------------------------------------------------------------------------
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 = 0.4113 r_free = 0.4113 target = 0.163655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.130511 restraints weight = 19163.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 2.42
r_work: 0.3582 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3443 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3486
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3486
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   4849  Z= 0.319
  Angle     :  0.600   6.909   6594  Z= 0.320
  Chirality :  0.040   0.150    739
  Planarity :  0.005   0.051    816
  Dihedral  :  6.795  56.837    685
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 23.75 %
    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:  0.47 (0.35), residues: 590
  helix:  1.75 (0.28), residues: 342
  sheet: -1.48 (0.68), residues: 59
  loop : -1.81 (0.40), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 107 
 HIS   0.004   0.001   HIS A 279 
 PHE   0.026   0.002   PHE A  48 
 TYR   0.014   0.002   TYR A 634 
 ARG   0.003   0.000   ARG B 102 

*********************** 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
  79 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 SER cc_start: 0.8439 (OUTLIER) cc_final: 0.8120 (p)
REVERT: A  211 CYS cc_start: 0.7331 (OUTLIER) cc_final: 0.7003 (m)
REVERT: A  266 ARG cc_start: 0.7574 (mtm180) cc_final: 0.7288 (mtm-85)
REVERT: A  374 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.8229 (m-10)
REVERT: B   31 ASP cc_start: 0.8065 (t0) cc_final: 0.7757 (t0)
REVERT: B   56 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7654 (mtp180)
REVERT: B  106 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7971 (ptpt)
  outliers start: 14
  outliers final: 4
  residues processed: 77
  average time/residue: 2.5598
  time to fit residues: 206.9403
Evaluate side-chains
  72 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
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  211 CYS
Chi-restraints excluded: chain A residue  214 GLN
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 9 optimal weight:    0.0770
   chunk 1 optimal weight:    0.9990
   chunk 55 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 3 optimal weight:    0.2980
   overall best weight:    0.5338

-------------------------------------------------------------------------------
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 = 0.4137 r_free = 0.4137 target = 0.165487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.133609 restraints weight = 17481.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 2.27
r_work: 0.3615 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3475 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3512
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3512 r_free = 0.3512    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3512
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4849  Z= 0.204
  Angle     :  0.567   7.191   6594  Z= 0.299
  Chirality :  0.038   0.149    739
  Planarity :  0.004   0.050    816
  Dihedral  :  6.136  43.010    681
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  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:  0.60 (0.35), residues: 590
  helix:  1.89 (0.28), residues: 340
  sheet: -1.46 (0.68), residues: 59
  loop : -1.80 (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   0.020   0.001   PHE A  48 
 TYR   0.010   0.001   TYR A 634 
 ARG   0.002   0.000   ARG B 100 

*********************** 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
  80 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8115 (p)
REVERT: A  211 CYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6963 (m)
REVERT: A  212 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.7080 (m-80)
REVERT: B   31 ASP cc_start: 0.8012 (t0) cc_final: 0.7801 (t0)
REVERT: B   56 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7694 (mtp180)
REVERT: B  106 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7958 (ptpt)
REVERT: B  115 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7968 (pt0)
  outliers start: 14
  outliers final: 5
  residues processed: 76
  average time/residue: 2.2663
  time to fit residues: 179.9054
Evaluate side-chains
  75 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
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  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 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:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 54 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4105 r_free = 0.4105 target = 0.162871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.131404 restraints weight = 16274.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 2.19
r_work: 0.3599 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3460 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3498
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    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 = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3498
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   4849  Z= 0.294
  Angle     :  0.601   7.145   6594  Z= 0.320
  Chirality :  0.040   0.151    739
  Planarity :  0.005   0.050    816
  Dihedral  :  6.349  42.536    681
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 23.35 %
    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:  0.39 (0.35), residues: 590
  helix:  1.61 (0.28), residues: 346
  sheet: -1.63 (0.67), residues: 59
  loop : -1.72 (0.41), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 279 
 PHE   0.026   0.002   PHE A  48 
 TYR   0.014   0.002   TYR A 634 
 ARG   0.003   0.000   ARG B 102 

*********************** 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
  84 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 1.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7588 (tt)
REVERT: A  198 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8095 (p)
REVERT: A  211 CYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6967 (m)
REVERT: A  374 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.8186 (m-10)
REVERT: B   31 ASP cc_start: 0.7986 (t0) cc_final: 0.7720 (t0)
REVERT: B   56 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7628 (mtp180)
REVERT: B  106 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7966 (ptpt)
  outliers start: 18
  outliers final: 5
  residues processed: 80
  average time/residue: 3.0123
  time to fit residues: 256.3864
Evaluate side-chains
  74 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
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  266 ARG
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 46 optimal weight:    0.3980
   chunk 28 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0970
   chunk 43 optimal weight:    0.9980
   chunk 36 optimal weight:    0.3980
   chunk 32 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.4178

-------------------------------------------------------------------------------
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 = 0.4144 r_free = 0.4144 target = 0.166007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.133509 restraints weight = 19148.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3778 rms_B_bonded: 2.37
r_work: 0.3622 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3485 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3527
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3527 r_free = 0.3527    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3527 r_free = 0.3527    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3527
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4849  Z= 0.183
  Angle     :  0.567   7.750   6594  Z= 0.299
  Chirality :  0.038   0.148    739
  Planarity :  0.004   0.050    816
  Dihedral  :  5.926  42.971    678
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  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:  0.63 (0.35), residues: 590
  helix:  1.91 (0.28), residues: 340
  sheet: -1.48 (0.68), residues: 59
  loop : -1.77 (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   0.010   0.001   TYR A 634 
 ARG   0.003   0.000   ARG B  67 

*********************** 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
  77 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 SER cc_start: 0.8443 (OUTLIER) cc_final: 0.8117 (p)
REVERT: A  211 CYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6906 (m)
REVERT: A  212 PHE cc_start: 0.7397 (m-80) cc_final: 0.7102 (m-80)
REVERT: B   56 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7681 (mtp180)
REVERT: B  106 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.7725 (ptpt)
REVERT: B  115 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7966 (pt0)
  outliers start: 10
  outliers final: 6
  residues processed: 75
  average time/residue: 1.9706
  time to fit residues: 155.6820
Evaluate side-chains
  75 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
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  198 SER
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  266 ARG
Chi-restraints excluded: chain A residue  276 LYS
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 58 optimal weight:    0.0670
   chunk 6 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 21 optimal weight:    0.3980
   chunk 36 optimal weight:    0.0010
   chunk 3 optimal weight:    0.9990
   chunk 4 optimal weight:    0.4980
   chunk 2 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 18 optimal weight:    0.1980
   overall best weight:    0.2324

-------------------------------------------------------------------------------
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 = 0.4166 r_free = 0.4166 target = 0.168213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.135680 restraints weight = 19902.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 2.43
r_work: 0.3651 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3511 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3552
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3552 r_free = 0.3552    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3552 r_free = 0.3552    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3552
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4849  Z= 0.155
  Angle     :  0.553   8.197   6594  Z= 0.293
  Chirality :  0.037   0.146    739
  Planarity :  0.004   0.049    816
  Dihedral  :  5.594  42.752    678
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 24.55 %
    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:  0.90 (0.36), residues: 590
  helix:  2.20 (0.29), residues: 334
  sheet: -1.31 (0.68), residues: 59
  loop : -1.67 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 291 
 PHE   0.013   0.001   PHE A  48 
 TYR   0.010   0.001   TYR A 634 
 ARG   0.001   0.000   ARG A 243 

********************** 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
  79 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 SER cc_start: 0.8445 (OUTLIER) cc_final: 0.8120 (p)
REVERT: A  211 CYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6852 (m)
REVERT: A  278 GLN cc_start: 0.7360 (tp40) cc_final: 0.7047 (tp40)
REVERT: A  374 PHE cc_start: 0.8432 (m-10) cc_final: 0.8032 (m-10)
REVERT: B   56 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7699 (mtp180)
  outliers start: 12
  outliers final: 5
  residues processed: 78
  average time/residue: 2.2748
  time to fit residues: 185.3485
Evaluate side-chains
  71 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
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  198 SER
Chi-restraints excluded: chain A residue  211 CYS
Chi-restraints excluded: chain A residue  266 ARG
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:    0.9980
   chunk 45 optimal weight:    0.0570
   chunk 55 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 54 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.6298

-------------------------------------------------------------------------------
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 = 0.4143 r_free = 0.4143 target = 0.165921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.133052 restraints weight = 19903.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3767 rms_B_bonded: 2.42
r_work: 0.3610 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
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 = 0.43   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 = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3517
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4849  Z= 0.230
  Angle     :  0.575   7.574   6594  Z= 0.305
  Chirality :  0.038   0.148    739
  Planarity :  0.004   0.049    816
  Dihedral  :  5.772  42.621    678
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 24.95 %
    Favored  : 72.85 %
  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:  0.78 (0.35), residues: 590
  helix:  2.07 (0.28), residues: 334
  sheet: -1.38 (0.68), residues: 59
  loop : -1.68 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 279 
 PHE   0.020   0.001   PHE A  48 
 TYR   0.013   0.001   TYR A 634 
 ARG   0.001   0.000   ARG B 102 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8771.85 seconds
wall clock time: 153 minutes 20.54 seconds (9200.54 seconds total)