Starting phenix.real_space_refine
on Sat Aug 23 03:40:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9biu_44602/08_2025/9biu_44602_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9biu_44602/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9biu_44602/08_2025/9biu_44602_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9biu_44602/08_2025/9biu_44602_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9biu_44602/08_2025/9biu_44602.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9biu_44602/08_2025/9biu_44602.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.036
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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.83, per 1000 atoms: 0.30
  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: 0.94
  Conformation dependent library (CDL) restraints added in 280.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.23
  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: 2.12

  Time building geometry restraints manager: 1.29 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:             6.410
  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:             0.070
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.380
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.810
-------------------------------------------------------------------------------
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 : 4.75
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  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
 ARG   0.002   0.000   ARG B  38 
 TYR   0.008   0.001   TYR A 183 
 PHE   0.009   0.001   PHE A  48 
 TRP   0.007   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 279 

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

*********************** 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  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 9
  residues processed: 77
  average time/residue: 0.8973
  time to fit residues: 72.7839
Evaluate side-chains
  75 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 PHE
Chi-restraints excluded: chain A residue   52 ASN
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 54 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.4980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0980
   chunk 58 optimal weight:    0.3980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.4134 r_free = 0.4134 target = 0.165717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.134203 restraints weight = 17030.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3793 rms_B_bonded: 2.24
r_work: 0.3621 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3483 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3526
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3526 r_free = 0.3526    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3526 r_free = 0.3526    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3526
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.0524

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= 0.144
  Angle     :  0.569   7.071   6598  Z= 0.300
  Chirality :  0.038   0.149    739
  Planarity :  0.004   0.050    816
  Dihedral  :  7.371  57.312    693
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 22.36 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.35), residues: 590
  helix:  1.95 (0.28), residues: 339
  sheet: -1.14 (0.70), residues: 59
  loop : -1.81 (0.41), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  38 
 TYR   0.014   0.001   TYR A 634 
 PHE   0.019   0.001   PHE A  48 
 TRP   0.007   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4849)
  covalent geometry    : angle       0.56747 ( 6594)
  SS BOND              : bond        0.00215 (    2)
  SS BOND              : angle       1.61297 (    4)
  hydrogen bonds       : bond        0.04938 (  276)
  hydrogen bonds       : angle       4.24469 (  797)

*********************** 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
  85 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 69
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: A  198 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8140 (p)
REVERT: A  374 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.8131 (m-10)
REVERT: B   56 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7597 (mtp180)
  outliers start: 16
  outliers final: 6
  residues processed: 78
  average time/residue: 0.8599
  time to fit residues: 70.5922
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  : 0.247 
-------------------------------------------------------------------------------
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 31 optimal weight:    0.0870
   chunk 53 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0970
   chunk 33 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.4956

-------------------------------------------------------------------------------
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 = 0.4134 r_free = 0.4134 target = 0.165939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.134416 restraints weight = 16961.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3782 rms_B_bonded: 2.24
r_work: 0.3636 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3500 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3538
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3538 r_free = 0.3538    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3538 r_free = 0.3538    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3538
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.0721

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= 0.137
  Angle     :  0.553   6.878   6598  Z= 0.291
  Chirality :  0.038   0.148    739
  Planarity :  0.004   0.049    816
  Dihedral  :  6.872  57.954    687
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 23.35 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.35), residues: 590
  helix:  1.97 (0.28), residues: 339
  sheet: -1.29 (0.69), residues: 59
  loop : -1.86 (0.41), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  38 
 TYR   0.011   0.001   TYR A 634 
 PHE   0.019   0.001   PHE A  48 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 4849)
  covalent geometry    : angle       0.55164 ( 6594)
  SS BOND              : bond        0.00128 (    2)
  SS BOND              : angle       1.61894 (    4)
  hydrogen bonds       : bond        0.04418 (  276)
  hydrogen bonds       : angle       4.08807 (  797)

*********************** 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
  77 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  198 SER cc_start: 0.8425 (OUTLIER) cc_final: 0.8124 (p)
REVERT: A  212 PHE cc_start: 0.7372 (m-80) cc_final: 0.7079 (m-80)
REVERT: A  374 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8090 (m-10)
REVERT: B   56 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7613 (mtp180)
REVERT: B  106 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7842 (ptpt)
  outliers start: 14
  outliers final: 5
  residues processed: 72
  average time/residue: 0.8912
  time to fit residues: 67.5461
Evaluate side-chains
  70 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
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 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 3 optimal weight:    0.9980
   chunk 56 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0060
   chunk 23 optimal weight:    0.0070
   chunk 39 optimal weight:    0.3980
   chunk 30 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.3814

-------------------------------------------------------------------------------
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 = 0.4145 r_free = 0.4145 target = 0.166513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.135894 restraints weight = 16076.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3805 rms_B_bonded: 2.14
r_work: 0.3658 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3531 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3573
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3573 r_free = 0.3573    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3573 r_free = 0.3573    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3573
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.0829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4851  Z= 0.120
  Angle     :  0.540   6.702   6598  Z= 0.283
  Chirality :  0.037   0.147    739
  Planarity :  0.004   0.047    816
  Dihedral  :  6.565  59.712    686
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 4.22
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.35), residues: 590
  helix:  2.02 (0.28), residues: 340
  sheet: -1.29 (0.69), residues: 59
  loop : -1.91 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  38 
 TYR   0.011   0.001   TYR A 634 
 PHE   0.016   0.001   PHE A  48 
 TRP   0.007   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 4849)
  covalent geometry    : angle       0.53885 ( 6594)
  SS BOND              : bond        0.00127 (    2)
  SS BOND              : angle       1.54555 (    4)
  hydrogen bonds       : bond        0.03971 (  276)
  hydrogen bonds       : angle       3.96328 (  797)

*********************** 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
  77 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A   99 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7598 (tt)
REVERT: A  198 SER cc_start: 0.8446 (OUTLIER) cc_final: 0.8149 (p)
REVERT: A  278 GLN cc_start: 0.7572 (tp40) cc_final: 0.7325 (tp40)
REVERT: B   31 ASP cc_start: 0.8110 (t0) cc_final: 0.7773 (t0)
REVERT: B   56 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7649 (mtp180)
REVERT: B  106 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7737 (ptpt)
  outliers start: 14
  outliers final: 4
  residues processed: 73
  average time/residue: 1.0263
  time to fit residues: 78.3886
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  : 0.240 
-------------------------------------------------------------------------------
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 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 18 optimal weight:    0.0670
   chunk 5 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0970
   chunk 33 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.6316

-------------------------------------------------------------------------------
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 = 0.165006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.133602 restraints weight = 16848.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 2.22
r_work: 0.3629 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3493 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3533
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3533 r_free = 0.3533    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3533 r_free = 0.3533    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3533
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1000

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= 0.154
  Angle     :  0.555   6.794   6598  Z= 0.293
  Chirality :  0.038   0.148    739
  Planarity :  0.005   0.048    816
  Dihedral  :  6.552  57.660    685
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 23.55 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.35), residues: 590
  helix:  1.97 (0.28), residues: 340
  sheet: -1.30 (0.68), residues: 59
  loop : -1.87 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 102 
 TYR   0.012   0.001   TYR A 634 
 PHE   0.021   0.001   PHE A  48 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 4849)
  covalent geometry    : angle       0.55410 ( 6594)
  SS BOND              : bond        0.00212 (    2)
  SS BOND              : angle       1.65549 (    4)
  hydrogen bonds       : bond        0.04297 (  276)
  hydrogen bonds       : angle       3.98076 (  797)

*********************** 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: 13
    poor density    : 64
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A   99 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7595 (tt)
REVERT: A  198 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.8119 (p)
REVERT: A  278 GLN cc_start: 0.7621 (tp40) cc_final: 0.7349 (tp40)
REVERT: A  374 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.8095 (m-10)
REVERT: B   31 ASP cc_start: 0.8068 (t0) cc_final: 0.7750 (t0)
REVERT: B   56 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7645 (mtp180)
REVERT: B  106 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8045 (ptpt)
REVERT: B  115 GLU cc_start: 0.8481 (pt0) cc_final: 0.7909 (mp0)
  outliers start: 13
  outliers final: 3
  residues processed: 73
  average time/residue: 1.0772
  time to fit residues: 82.4355
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  : 0.288 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0970
   chunk 25 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.4125 r_free = 0.4125 target = 0.164984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.132701 restraints weight = 19302.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3771 rms_B_bonded: 2.39
r_work: 0.3619 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3480 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3480
-------------------------------------------------------------------------------
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 = 0.42   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 = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3517
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.1088

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= 0.144
  Angle     :  0.552   6.720   6598  Z= 0.290
  Chirality :  0.038   0.148    739
  Planarity :  0.004   0.049    816
  Dihedral  :  6.002  43.041    681
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 23.35 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.35), residues: 590
  helix:  1.96 (0.28), residues: 340
  sheet: -1.33 (0.68), residues: 59
  loop : -1.82 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 102 
 TYR   0.011   0.001   TYR A 634 
 PHE   0.020   0.001   PHE A  48 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 4849)
  covalent geometry    : angle       0.55099 ( 6594)
  SS BOND              : bond        0.00171 (    2)
  SS BOND              : angle       1.63459 (    4)
  hydrogen bonds       : bond        0.04197 (  276)
  hydrogen bonds       : angle       3.96065 (  797)

*********************** 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
  78 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A   99 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7589 (tt)
REVERT: A  198 SER cc_start: 0.8429 (OUTLIER) cc_final: 0.8125 (p)
REVERT: A  278 GLN cc_start: 0.7656 (tp40) cc_final: 0.7341 (tp40)
REVERT: B   31 ASP cc_start: 0.8136 (t0) cc_final: 0.7853 (t0)
REVERT: B   56 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7673 (mtp180)
REVERT: B  106 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8118 (ptpt)
REVERT: B  115 GLU cc_start: 0.8491 (pt0) cc_final: 0.7917 (mp0)
  outliers start: 13
  outliers final: 4
  residues processed: 73
  average time/residue: 1.1471
  time to fit residues: 87.3432
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  : 0.251 
-------------------------------------------------------------------------------
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 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 15 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 34 optimal weight:    0.4980
   chunk 49 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4115 r_free = 0.4115 target = 0.163989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.131769 restraints weight = 17789.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3756 rms_B_bonded: 2.31
r_work: 0.3604 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3464 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3501
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3501 r_free = 0.3501    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 = 0.3501 r_free = 0.3501    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3501
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4851  Z= 0.181
  Angle     :  0.580   6.830   6598  Z= 0.307
  Chirality :  0.039   0.150    739
  Planarity :  0.005   0.050    816
  Dihedral  :  6.180  42.784    681
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 23.55 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.35), residues: 590
  helix:  1.85 (0.28), residues: 340
  sheet: -1.40 (0.68), residues: 59
  loop : -1.83 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 102 
 TYR   0.012   0.001   TYR A 634 
 PHE   0.024   0.002   PHE A  48 
 TRP   0.011   0.001   TRP A 107 
 HIS   0.004   0.001   HIS A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 4849)
  covalent geometry    : angle       0.57832 ( 6594)
  SS BOND              : bond        0.00274 (    2)
  SS BOND              : angle       1.71492 (    4)
  hydrogen bonds       : bond        0.04553 (  276)
  hydrogen bonds       : angle       4.02580 (  797)

*********************** 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: 12
    poor density    : 66
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7610 (tt)
REVERT: A  198 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.8095 (p)
REVERT: A  278 GLN cc_start: 0.7686 (tp40) cc_final: 0.7362 (tp40)
REVERT: A  374 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.8145 (m-10)
REVERT: B   31 ASP cc_start: 0.8091 (t0) cc_final: 0.7809 (t0)
REVERT: B   56 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7650 (mtp180)
REVERT: B  106 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7996 (ptpt)
  outliers start: 12
  outliers final: 3
  residues processed: 75
  average time/residue: 1.2086
  time to fit residues: 94.4160
Evaluate side-chains
  73 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 0 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0970
   chunk 11 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.7178

-------------------------------------------------------------------------------
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 = 0.4124 r_free = 0.4124 target = 0.164668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.132272 restraints weight = 17695.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 2.32
r_work: 0.3609 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3468 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3468
-------------------------------------------------------------------------------
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 = 0.43   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 = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3505
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.1278

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= 0.168
  Angle     :  0.575   6.789   6598  Z= 0.304
  Chirality :  0.039   0.150    739
  Planarity :  0.005   0.049    816
  Dihedral  :  5.993  42.704    678
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 24.35 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.35), residues: 590
  helix:  1.80 (0.28), residues: 342
  sheet: -1.45 (0.68), residues: 59
  loop : -1.73 (0.41), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 100 
 TYR   0.011   0.001   TYR A 634 
 PHE   0.023   0.001   PHE A  48 
 TRP   0.011   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 4849)
  covalent geometry    : angle       0.57356 ( 6594)
  SS BOND              : bond        0.00226 (    2)
  SS BOND              : angle       1.66812 (    4)
  hydrogen bonds       : bond        0.04441 (  276)
  hydrogen bonds       : angle       4.01113 (  797)

*********************** 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
  77 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7589 (tt)
REVERT: A  198 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.8098 (p)
REVERT: A  212 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.7101 (m-80)
REVERT: A  278 GLN cc_start: 0.7693 (tp40) cc_final: 0.7377 (tp40)
REVERT: A  374 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.8194 (m-10)
REVERT: B   31 ASP cc_start: 0.8034 (t0) cc_final: 0.7781 (t0)
REVERT: B   56 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7645 (mtp180)
REVERT: B  106 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7947 (ptpt)
REVERT: B  115 GLU cc_start: 0.8492 (pt0) cc_final: 0.7949 (mp0)
  outliers start: 11
  outliers final: 4
  residues processed: 74
  average time/residue: 1.0665
  time to fit residues: 82.2369
Evaluate side-chains
  74 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
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  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 5 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 31 optimal weight:    0.1980
   chunk 18 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 53 optimal weight:    0.4980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4129 r_free = 0.4129 target = 0.164598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.133041 restraints weight = 17591.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3771 rms_B_bonded: 2.25
r_work: 0.3617 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3478 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3516
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3516 r_free = 0.3516    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 = 0.3516 r_free = 0.3516    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3516
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4851  Z= 0.153
  Angle     :  0.565   6.715   6598  Z= 0.300
  Chirality :  0.038   0.148    739
  Planarity :  0.004   0.049    816
  Dihedral  :  5.955  42.765    678
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.35), residues: 590
  helix:  1.83 (0.28), residues: 342
  sheet: -1.41 (0.68), residues: 59
  loop : -1.72 (0.41), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 102 
 TYR   0.011   0.001   TYR A 634 
 PHE   0.021   0.001   PHE A  48 
 TRP   0.010   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 4849)
  covalent geometry    : angle       0.56413 ( 6594)
  SS BOND              : bond        0.00194 (    2)
  SS BOND              : angle       1.60989 (    4)
  hydrogen bonds       : bond        0.04301 (  276)
  hydrogen bonds       : angle       3.97289 (  797)

*********************** 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
  80 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7573 (tt)
REVERT: A  198 SER cc_start: 0.8412 (OUTLIER) cc_final: 0.8100 (p)
REVERT: A  212 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.7086 (m-80)
REVERT: A  278 GLN cc_start: 0.7724 (tp40) cc_final: 0.7404 (tp40)
REVERT: A  374 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8182 (m-10)
REVERT: B   31 ASP cc_start: 0.7977 (t0) cc_final: 0.7746 (t0)
REVERT: B   56 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7634 (mtp180)
REVERT: B  106 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7890 (ptpt)
REVERT: B  115 GLU cc_start: 0.8467 (pt0) cc_final: 0.7930 (mp0)
  outliers start: 12
  outliers final: 3
  residues processed: 77
  average time/residue: 1.1360
  time to fit residues: 91.0065
Evaluate side-chains
  75 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 9 optimal weight:    0.0980
   chunk 13 optimal weight:    0.6980
   chunk 41 optimal weight:    0.1980
   chunk 50 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 58 optimal weight:    0.3980
   chunk 3 optimal weight:    0.6980
   chunk 57 optimal weight:    0.2980
   overall best weight:    0.3380

-------------------------------------------------------------------------------
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 = 0.4148 r_free = 0.4148 target = 0.166879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.134970 restraints weight = 17812.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 2.30
r_work: 0.3648 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3509 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3545
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3545
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.1299

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     :  0.543   6.546   6598  Z= 0.286
  Chirality :  0.037   0.146    739
  Planarity :  0.004   0.049    816
  Dihedral  :  5.715  42.946    678
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 25.15 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.35), residues: 590
  helix:  2.13 (0.28), residues: 334
  sheet: -1.28 (0.69), residues: 59
  loop : -1.59 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  38 
 TYR   0.010   0.001   TYR A 634 
 PHE   0.016   0.001   PHE A  48 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 4849)
  covalent geometry    : angle       0.54165 ( 6594)
  SS BOND              : bond        0.00093 (    2)
  SS BOND              : angle       1.51114 (    4)
  hydrogen bonds       : bond        0.03843 (  276)
  hydrogen bonds       : angle       3.86130 (  797)

********************** 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
  76 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  198 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8131 (p)
REVERT: A  278 GLN cc_start: 0.7788 (tp40) cc_final: 0.7455 (tp40)
REVERT: B   56 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7669 (mtp180)
REVERT: B  115 GLU cc_start: 0.8452 (pt0) cc_final: 0.7926 (mp0)
  outliers start: 9
  outliers final: 4
  residues processed: 72
  average time/residue: 1.0981
  time to fit residues: 82.1750
Evaluate side-chains
  72 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
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  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 3 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 43 optimal weight:    0.2980
   chunk 23 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0670
   chunk 50 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.4918

-------------------------------------------------------------------------------
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 = 0.166251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.134464 restraints weight = 16867.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3792 rms_B_bonded: 2.24
r_work: 0.3641 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3504 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    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 = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.1316

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= 0.136
  Angle     :  0.555   6.624   6598  Z= 0.294
  Chirality :  0.038   0.147    739
  Planarity :  0.004   0.049    816
  Dihedral  :  5.738  42.830    678
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 25.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.35), residues: 590
  helix:  2.10 (0.28), residues: 334
  sheet: -1.26 (0.69), residues: 59
  loop : -1.64 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 102 
 TYR   0.012   0.001   TYR A 634 
 PHE   0.018   0.001   PHE A  48 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.003   0.001   HIS A 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4849)
  covalent geometry    : angle       0.55427 ( 6594)
  SS BOND              : bond        0.00136 (    2)
  SS BOND              : angle       1.56388 (    4)
  hydrogen bonds       : bond        0.04017 (  276)
  hydrogen bonds       : angle       3.87085 (  797)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3987.81 seconds
wall clock time: 68 minutes 7.85 seconds (4087.85 seconds total)