Starting phenix.real_space_refine
on Tue Feb  3 14:32:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kl5_62400/02_2026/9kl5_62400.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kl5_62400/02_2026/9kl5_62400.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kl5_62400/02_2026/9kl5_62400.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kl5_62400/02_2026/9kl5_62400.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kl5_62400/02_2026/9kl5_62400.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kl5_62400/02_2026/9kl5_62400.map"
  }
  resolution = 3.33
  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=   0.015
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: 5
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     Cl      1      4.86       5
     C    2395      2.51       5
     N     622      2.21       5
     O     634      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3683
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 474, 3663
          Classifications: {'peptide': 474}
          Link IDs: {'PTRANS': 24, 'TRANS': 449}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 20
          Unusual residues: {' CL': 1, 'RTO': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 0.89, per 1000 atoms: 0.24
  Number of scatterers: 3683
  At special positions: 0
  Unit cell: (96.39, 60.75, 71.28, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      31     16.00
     O     634      8.00
     N     622      7.00
     C    2395      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  49 " - pdb=" SG  CYS A 105 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  78 " - pdb=" SG  CYS A 128 " distance=2.02

  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: 0.30
  Conformation dependent library (CDL) restraints added in 139.6 milliseconds
  

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  876

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 1 sheets defined
      80.6% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
      removed outlier: 3.631A  pdb=" N   LEU A   6 " --> pdb=" O   ALA A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 26
    Processing helix  chain 'A' and resid 27 through 30
    Processing helix  chain 'A' and resid 31 through 36
    Processing helix  chain 'A' and resid 37 through 42
    Processing helix  chain 'A' and resid 119 through 125
    Processing helix  chain 'A' and resid 130 through 160
      removed outlier: 4.051A  pdb=" N   ARG A 134 " --> pdb=" O   HIS A 130 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLN A 135 " --> pdb=" O   ARG A 131 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   MET A 150 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   TYR A 154 " --> pdb=" O   MET A 150 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASP A 157 " --> pdb=" O   GLY A 153 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ARG A 158 " --> pdb=" O   TYR A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 180
      removed outlier: 3.922A  pdb=" N   VAL A 164 " --> pdb=" O   GLY A 160 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA A 180 " --> pdb=" O   GLY A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 212
      removed outlier: 3.771A  pdb=" N   SER A 195 " --> pdb=" O   PHE A 191 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   GLY A 201 " --> pdb=" O   MET A 197 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER A 203 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   MET A 207 " --> pdb=" O   SER A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 217
      No H-bonds generated for 'chain 'A' and resid 215 through 217'
    Processing helix  chain 'A' and resid 218 through 244
      removed outlier: 3.514A  pdb=" N   THR A 224 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLN A 234 " --> pdb=" O   TYR A 230 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   PHE A 235 " --> pdb=" O   SER A 231 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ALA A 243 " --> pdb=" O   GLY A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 256
    Processing helix  chain 'A' and resid 256 through 264
      removed outlier: 4.175A  pdb=" N   ALA A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   TYR A 264 " --> pdb=" O   ALA A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 268
      removed outlier: 3.731A  pdb=" N   PHE A 268 " --> pdb=" O   SER A 265 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 265 through 268'
    Processing helix  chain 'A' and resid 271 through 278
    Processing helix  chain 'A' and resid 280 through 296
    Processing helix  chain 'A' and resid 297 through 303
      removed outlier: 3.553A  pdb=" N   LYS A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 313
    Processing helix  chain 'A' and resid 326 through 332
      removed outlier: 3.613A  pdb=" N   LEU A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 354
      removed outlier: 3.523A  pdb=" N   HIS A 337 " --> pdb=" O   PRO A 333 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   LEU A 338 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   MET A 344 " --> pdb=" O   LEU A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 377
      removed outlier: 4.164A  pdb=" N   VAL A 372 " --> pdb=" O   TYR A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 392
      removed outlier: 3.562A  pdb=" N   ASN A 390 " --> pdb=" O   PHE A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 415
      removed outlier: 3.633A  pdb=" N   ALA A 405 " --> pdb=" O   ALA A 401 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 449
      removed outlier: 3.577A  pdb=" N   ASN A 439 " --> pdb=" O   ALA A 435 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   TYR A 449 " --> pdb=" O   THR A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 477
      removed outlier: 3.568A  pdb=" N   MET A 464 " --> pdb=" O   MET A 460 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ALA A 465 " --> pdb=" O   GLY A 461 " (cutoff:3.500A)
      Proline residue:  A 473  - end of helix
    Processing helix  chain 'A' and resid 478 through 481
    Processing helix  chain 'A' and resid 484 through 499
      removed outlier: 3.570A  pdb=" N   PHE A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
      Proline residue:  A 494  - end of helix
    Processing helix  chain 'A' and resid 500 through 504
      removed outlier: 3.667A  pdb=" N   LEU A 504 " --> pdb=" O   THR A 501 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49

    236 hydrogen bonds defined for protein.
    699 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: 0.33

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1159
        1.34 -     1.46: 912
        1.46 -     1.58: 1648
        1.58 -     1.70: 0
        1.70 -     1.82: 49
  Bond restraints: 3768
  Sorted by residual:
  bond pdb=" N04 RTO A 601 "
       pdb=" S08 RTO A 601 "
    ideal  model  delta    sigma   weight residual
    1.625  1.712 -0.087 2.00e-02 2.50e+03 1.89e+01
  bond pdb=" N   LYS A 382 "
       pdb=" CA  LYS A 382 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.23e-02 6.61e+03 5.41e+00
  bond pdb=" C11 RTO A 601 "
       pdb=" S08 RTO A 601 "
    ideal  model  delta    sigma   weight residual
    1.776  1.820 -0.044 2.00e-02 2.50e+03 4.83e+00
  bond pdb=" N   ARG A 466 "
       pdb=" CA  ARG A 466 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.028 1.28e-02 6.10e+03 4.66e+00
  bond pdb=" CB  CYS A  78 "
       pdb=" SG  CYS A  78 "
    ideal  model  delta    sigma   weight residual
    1.808  1.776  0.032 3.30e-02 9.18e+02 9.54e-01
  ... (remaining 3763 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.62: 5103
        3.62 -     7.23: 22
        7.23 -    10.85: 0
       10.85 -    14.46: 0
       14.46 -    18.08: 1
  Bond angle restraints: 5126
  Sorted by residual:
  angle pdb=" O09 RTO A 601 "
        pdb=" S08 RTO A 601 "
        pdb=" O10 RTO A 601 "
      ideal   model   delta    sigma   weight residual
     119.19  101.11   18.08 3.00e+00 1.11e-01 3.63e+01
  angle pdb=" C   LEU A 126 "
        pdb=" N   VAL A 127 "
        pdb=" CA  VAL A 127 "
      ideal   model   delta    sigma   weight residual
     122.97  119.86    3.11 9.80e-01 1.04e+00 1.01e+01
  angle pdb=" CA  LYS A 382 "
        pdb=" C   LYS A 382 "
        pdb=" O   LYS A 382 "
      ideal   model   delta    sigma   weight residual
     120.42  117.99    2.43 1.06e+00 8.90e-01 5.28e+00
  angle pdb=" N   ARG A 466 "
        pdb=" CA  ARG A 466 "
        pdb=" C   ARG A 466 "
      ideal   model   delta    sigma   weight residual
     111.82  109.20    2.62 1.16e+00 7.43e-01 5.08e+00
  angle pdb=" O18 RTO A 601 "
        pdb=" C17 RTO A 601 "
        pdb=" O19 RTO A 601 "
      ideal   model   delta    sigma   weight residual
     126.54  120.07    6.47 3.00e+00 1.11e-01 4.65e+00
  ... (remaining 5121 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 1953
       17.90 -    35.81: 205
       35.81 -    53.71: 63
       53.71 -    71.61: 13
       71.61 -    89.51: 3
  Dihedral angle restraints: 2237
    sinusoidal: 875
      harmonic: 1362
  Sorted by residual:
  dihedral pdb=" CB  CYS A  49 "
           pdb=" SG  CYS A  49 "
           pdb=" SG  CYS A 105 "
           pdb=" CB  CYS A 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -165.51   79.51     1      1.00e+01 1.00e-02 7.85e+01
  dihedral pdb=" CB  GLU A 270 "
           pdb=" CG  GLU A 270 "
           pdb=" CD  GLU A 270 "
           pdb=" OE1 GLU A 270 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.11  -85.11     1      3.00e+01 1.11e-03 9.76e+00
  dihedral pdb=" CA  GLN A   8 "
           pdb=" CB  GLN A   8 "
           pdb=" CG  GLN A   8 "
           pdb=" CD  GLN A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.99   58.99     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 2234 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 364
       0.032 -    0.063: 178
       0.063 -    0.095: 32
       0.095 -    0.126: 21
       0.126 -    0.158: 2
  Chirality restraints: 597
  Sorted by residual:
  chirality pdb=" CG  LEU A 345 "
            pdb=" CB  LEU A 345 "
            pdb=" CD1 LEU A 345 "
            pdb=" CD2 LEU A 345 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.24e-01
  chirality pdb=" CA  ILE A 415 "
            pdb=" N   ILE A 415 "
            pdb=" C   ILE A 415 "
            pdb=" CB  ILE A 415 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.18e-01
  chirality pdb=" CA  ILE A 110 "
            pdb=" N   ILE A 110 "
            pdb=" C   ILE A 110 "
            pdb=" CB  ILE A 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.58e-01
  ... (remaining 594 not shown)

  Planarity restraints: 638
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 453 "   -0.008 2.00e-02 2.50e+03   1.59e-02 2.52e+00
        pdb=" C   ILE A 453 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ILE A 453 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ARG A 454 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 418 "    0.006 2.00e-02 2.50e+03   1.21e-02 1.46e+00
        pdb=" CG  ASP A 418 "   -0.021 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 418 "    0.008 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 418 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 444 "    0.009 2.00e-02 2.50e+03   8.34e-03 1.39e+00
        pdb=" CG  TYR A 444 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 444 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 444 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 444 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 444 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 444 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 444 "    0.001 2.00e-02 2.50e+03
  ... (remaining 635 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 1297
        2.85 -     3.36: 3592
        3.36 -     3.87: 6026
        3.87 -     4.39: 6903
        4.39 -     4.90: 11912
  Nonbonded interactions: 29730
  Sorted by model distance:
  nonbonded pdb=" O   GLN A 314 "
            pdb=" OG1 THR A 318 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" NH1 ARG A  80 "
            pdb=" OD1 ASP A 107 "
     model   vdw
     2.343 3.120
  nonbonded pdb=" O   SER A 472 "
            pdb=" OH  TYR A 490 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" OG  SER A 231 "
            pdb=" OD2 ASP A 378 "
     model   vdw
     2.372 3.040
  nonbonded pdb=" O   CYS A 206 "
            pdb=" ND2 ASN A 210 "
     model   vdw
     2.372 3.120
  ... (remaining 29725 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.550
  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:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.270
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:0.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   3770  Z= 0.196
  Angle     :  0.625  18.079   5130  Z= 0.289
  Chirality :  0.039   0.158    597
  Planarity :  0.004   0.026    638
  Dihedral  : 16.280  89.515   1355
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 21.83 %
    Favored  : 78.17 %
  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 are not related in a simple way.
  whole:  0.07 (0.40), residues: 466
  helix:  0.16 (0.28), residues: 348
  sheet:  0.22 (2.06), residues: 10
  loop :  0.16 (0.67), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 219 
 TYR   0.020   0.002   TYR A 444 
 PHE   0.008   0.001   PHE A 235 
 TRP   0.009   0.001   TRP A  66 
 HIS   0.003   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 3768)
  covalent geometry    : angle       0.62329 ( 5126)
  SS BOND              : bond        0.00785 (    2)
  SS BOND              : angle       1.87409 (    4)
  hydrogen bonds       : bond        0.25276 (  236)
  hydrogen bonds       : angle       7.94720 (  699)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.139 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0621
  time to fit residues: 4.1458
Evaluate side-chains
  53 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  18 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.126226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.099233 restraints weight = 4915.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 2.33
r_work: 0.2986 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2847 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.1209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3770  Z= 0.155
  Angle     :  0.564   6.631   5130  Z= 0.283
  Chirality :  0.039   0.127    597
  Planarity :  0.004   0.026    638
  Dihedral  :  6.834  58.844    535
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 19.54 %
    Favored  : 77.66 %
  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 are not related in a simple way.
  whole:  1.39 (0.41), residues: 466
  helix:  1.13 (0.28), residues: 356
  sheet:  0.07 (1.93), residues: 10
  loop :  0.62 (0.72), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.016   0.001   TYR A 444 
 PHE   0.010   0.001   PHE A 258 
 TRP   0.011   0.002   TRP A 346 
 HIS   0.004   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 3768)
  covalent geometry    : angle       0.56359 ( 5126)
  SS BOND              : bond        0.00684 (    2)
  SS BOND              : angle       1.15487 (    4)
  hydrogen bonds       : bond        0.05370 (  236)
  hydrogen bonds       : angle       4.84854 (  699)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A   31 MET cc_start: 0.8683 (tpt) cc_final: 0.8470 (mmm)
REVERT: A  202 ILE cc_start: 0.7623 (tt) cc_final: 0.7384 (mt)
REVERT: A  270 GLU cc_start: 0.8050 (tp30) cc_final: 0.7833 (tp30)
REVERT: A  293 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8200 (mtp85)
REVERT: A  344 MET cc_start: 0.8347 (tpt) cc_final: 0.8085 (tpp)
REVERT: A  503 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8250 (mm)
  outliers start: 11
  outliers final: 4
  residues processed: 63
  average time/residue: 0.0559
  time to fit residues: 4.6410
Evaluate side-chains
  55 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  293 ARG
Chi-restraints excluded: chain A residue  378 ASP
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  503 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 36 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0970
   chunk 2 optimal weight:    0.0000
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.3382

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

Flipped N/Q/H residues before XYZ refinement:
A  48 HIS
A 168 ASN
A 398 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.130879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.103811 restraints weight = 4764.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.32
r_work: 0.3046 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3770  Z= 0.108
  Angle     :  0.490   5.939   5130  Z= 0.239
  Chirality :  0.037   0.127    597
  Planarity :  0.003   0.024    638
  Dihedral  :  6.252  53.926    535
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 21.07 %
    Favored  : 76.40 %
  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 are not related in a simple way.
  whole:  1.81 (0.42), residues: 466
  helix:  1.48 (0.29), residues: 362
  sheet:  0.64 (2.07), residues: 10
  loop :  0.46 (0.76), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.012   0.001   TYR A 444 
 PHE   0.006   0.001   PHE A 339 
 TRP   0.010   0.001   TRP A 274 
 HIS   0.001   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 3768)
  covalent geometry    : angle       0.48886 ( 5126)
  SS BOND              : bond        0.00486 (    2)
  SS BOND              : angle       1.12052 (    4)
  hydrogen bonds       : bond        0.03910 (  236)
  hydrogen bonds       : angle       4.19966 (  699)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A    5 ASP cc_start: 0.8947 (m-30) cc_final: 0.8718 (t0)
REVERT: A   66 TRP cc_start: 0.7100 (m100) cc_final: 0.6826 (m100)
REVERT: A  293 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8159 (mtp85)
  outliers start: 10
  outliers final: 3
  residues processed: 60
  average time/residue: 0.0512
  time to fit residues: 3.8941
Evaluate side-chains
  54 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  293 ARG
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  438 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 18 optimal weight:    0.4980
   chunk 41 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3518 r_free = 0.3518 target = 0.130731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.103403 restraints weight = 4780.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 2.30
r_work: 0.3022 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3770  Z= 0.144
  Angle     :  0.511   5.875   5130  Z= 0.251
  Chirality :  0.039   0.149    597
  Planarity :  0.003   0.025    638
  Dihedral  :  6.254  53.392    535
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 19.80 %
    Favored  : 77.41 %
  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 are not related in a simple way.
  whole:  1.88 (0.42), residues: 466
  helix:  1.50 (0.29), residues: 363
  sheet:  0.54 (1.97), residues: 10
  loop :  0.59 (0.76), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 454 
 TYR   0.012   0.001   TYR A 264 
 PHE   0.009   0.001   PHE A 386 
 TRP   0.009   0.001   TRP A 247 
 HIS   0.003   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 3768)
  covalent geometry    : angle       0.51037 ( 5126)
  SS BOND              : bond        0.00691 (    2)
  SS BOND              : angle       1.19297 (    4)
  hydrogen bonds       : bond        0.04008 (  236)
  hydrogen bonds       : angle       4.16058 (  699)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.090 
Fit side-chains
REVERT: A    5 ASP cc_start: 0.8962 (m-30) cc_final: 0.8734 (t0)
REVERT: A   66 TRP cc_start: 0.7143 (m100) cc_final: 0.6919 (m100)
REVERT: A  112 ASP cc_start: 0.8346 (t0) cc_final: 0.8043 (t0)
  outliers start: 11
  outliers final: 8
  residues processed: 65
  average time/residue: 0.0342
  time to fit residues: 3.0684
Evaluate side-chains
  59 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  500 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 361 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.130816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.103421 restraints weight = 4749.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 2.30
r_work: 0.3026 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3770  Z= 0.149
  Angle     :  0.520   5.211   5130  Z= 0.258
  Chirality :  0.040   0.165    597
  Planarity :  0.004   0.025    638
  Dihedral  :  6.252  52.718    535
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 19.80 %
    Favored  : 76.90 %
  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 are not related in a simple way.
  whole:  1.95 (0.42), residues: 466
  helix:  1.52 (0.29), residues: 364
  sheet:  0.46 (1.90), residues: 10
  loop :  0.77 (0.79), residues: 92

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 219 
 TYR   0.012   0.001   TYR A 264 
 PHE   0.009   0.001   PHE A 235 
 TRP   0.009   0.001   TRP A 247 
 HIS   0.003   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 3768)
  covalent geometry    : angle       0.51587 ( 5126)
  SS BOND              : bond        0.00464 (    2)
  SS BOND              : angle       2.30465 (    4)
  hydrogen bonds       : bond        0.03981 (  236)
  hydrogen bonds       : angle       4.12128 (  699)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A    5 ASP cc_start: 0.8939 (m-30) cc_final: 0.8724 (t0)
REVERT: A   31 MET cc_start: 0.8675 (mmm) cc_final: 0.8388 (mmm)
REVERT: A  112 ASP cc_start: 0.8359 (t0) cc_final: 0.8043 (t0)
REVERT: A  293 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8219 (mtp85)
  outliers start: 13
  outliers final: 9
  residues processed: 64
  average time/residue: 0.0590
  time to fit residues: 4.9027
Evaluate side-chains
  61 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  293 ARG
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  500 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 5 optimal weight:    0.2980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 361 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.129329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.102128 restraints weight = 4815.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 2.30
r_work: 0.3030 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3770  Z= 0.142
  Angle     :  0.507   5.420   5130  Z= 0.251
  Chirality :  0.039   0.136    597
  Planarity :  0.003   0.025    638
  Dihedral  :  6.252  51.824    535
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 20.05 %
    Favored  : 76.40 %
  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 are not related in a simple way.
  whole:  2.05 (0.42), residues: 466
  helix:  1.58 (0.29), residues: 363
  sheet:  0.35 (1.84), residues: 10
  loop :  0.87 (0.79), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  80 
 TYR   0.012   0.001   TYR A 264 
 PHE   0.008   0.001   PHE A 235 
 TRP   0.011   0.001   TRP A  66 
 HIS   0.003   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 3768)
  covalent geometry    : angle       0.50327 ( 5126)
  SS BOND              : bond        0.00736 (    2)
  SS BOND              : angle       2.34850 (    4)
  hydrogen bonds       : bond        0.03892 (  236)
  hydrogen bonds       : angle       4.08315 (  699)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A    5 ASP cc_start: 0.8923 (m-30) cc_final: 0.8722 (t0)
REVERT: A   31 MET cc_start: 0.8691 (mmm) cc_final: 0.8401 (mmm)
REVERT: A  112 ASP cc_start: 0.8308 (t0) cc_final: 0.7997 (t0)
REVERT: A  293 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8213 (mtp85)
  outliers start: 14
  outliers final: 10
  residues processed: 63
  average time/residue: 0.0595
  time to fit residues: 4.8903
Evaluate side-chains
  62 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  293 ARG
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  500 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 18 optimal weight:    0.4980
   chunk 25 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0670
   chunk 30 optimal weight:    0.7980
   chunk 1 optimal weight:    0.2980
   chunk 46 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
A 361 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.130883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.103335 restraints weight = 4914.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.34
r_work: 0.3035 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3770  Z= 0.118
  Angle     :  0.496   5.821   5130  Z= 0.245
  Chirality :  0.038   0.131    597
  Planarity :  0.003   0.025    638
  Dihedral  :  6.208  52.278    535
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 20.81 %
    Favored  : 76.65 %
  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 are not related in a simple way.
  whole:  2.14 (0.42), residues: 466
  helix:  1.65 (0.29), residues: 363
  sheet:  0.45 (1.87), residues: 10
  loop :  0.92 (0.79), residues: 93

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  69 
 TYR   0.011   0.001   TYR A 264 
 PHE   0.007   0.001   PHE A 235 
 TRP   0.009   0.001   TRP A  66 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 3768)
  covalent geometry    : angle       0.49377 ( 5126)
  SS BOND              : bond        0.00655 (    2)
  SS BOND              : angle       1.77834 (    4)
  hydrogen bonds       : bond        0.03679 (  236)
  hydrogen bonds       : angle       4.01120 (  699)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A    5 ASP cc_start: 0.8906 (m-30) cc_final: 0.8701 (t0)
REVERT: A   31 MET cc_start: 0.8670 (mmm) cc_final: 0.8362 (mmm)
REVERT: A  112 ASP cc_start: 0.8323 (t0) cc_final: 0.8014 (t0)
REVERT: A  293 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8185 (mtp85)
  outliers start: 10
  outliers final: 7
  residues processed: 61
  average time/residue: 0.0612
  time to fit residues: 4.8375
Evaluate side-chains
  60 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 GLU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  293 ARG
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  500 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 24 optimal weight:    0.2980
   chunk 16 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 23 optimal weight:    0.1980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 361 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.130454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.103353 restraints weight = 4830.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 2.31
r_work: 0.3054 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3770  Z= 0.123
  Angle     :  0.502   5.969   5130  Z= 0.248
  Chirality :  0.038   0.131    597
  Planarity :  0.003   0.026    638
  Dihedral  :  6.195  52.510    535
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 21.57 %
    Favored  : 76.14 %
  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 are not related in a simple way.
  whole:  2.21 (0.42), residues: 466
  helix:  1.70 (0.29), residues: 362
  sheet:  0.59 (1.93), residues: 10
  loop :  0.90 (0.77), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  69 
 TYR   0.011   0.001   TYR A 264 
 PHE   0.030   0.001   PHE A 351 
 TRP   0.010   0.001   TRP A  66 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 3768)
  covalent geometry    : angle       0.49897 ( 5126)
  SS BOND              : bond        0.00704 (    2)
  SS BOND              : angle       1.88744 (    4)
  hydrogen bonds       : bond        0.03669 (  236)
  hydrogen bonds       : angle       3.98723 (  699)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A    5 ASP cc_start: 0.8918 (m-30) cc_final: 0.8707 (t0)
REVERT: A  112 ASP cc_start: 0.8331 (t0) cc_final: 0.8035 (t0)
REVERT: A  293 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8200 (mtp85)
  outliers start: 9
  outliers final: 6
  residues processed: 61
  average time/residue: 0.0402
  time to fit residues: 3.2637
Evaluate side-chains
  58 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  293 ARG
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  500 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 25 optimal weight:    0.0370
   chunk 39 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0980
   chunk 46 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 7 optimal weight:    7.9990
   overall best weight:    0.4058

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

Flipped N/Q/H residues before XYZ refinement:
A 361 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.133208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.106010 restraints weight = 4800.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.31
r_work: 0.3031 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3770  Z= 0.115
  Angle     :  0.498   6.249   5130  Z= 0.245
  Chirality :  0.038   0.130    597
  Planarity :  0.003   0.026    638
  Dihedral  :  6.156  52.883    535
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 22.08 %
    Favored  : 76.14 %
  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 are not related in a simple way.
  whole:  2.27 (0.42), residues: 466
  helix:  1.75 (0.29), residues: 362
  sheet:  0.58 (1.92), residues: 10
  loop :  0.92 (0.77), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  69 
 TYR   0.010   0.001   TYR A 264 
 PHE   0.030   0.001   PHE A 351 
 TRP   0.011   0.001   TRP A  66 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 3768)
  covalent geometry    : angle       0.49661 ( 5126)
  SS BOND              : bond        0.00671 (    2)
  SS BOND              : angle       1.56703 (    4)
  hydrogen bonds       : bond        0.03552 (  236)
  hydrogen bonds       : angle       3.96171 (  699)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A  112 ASP cc_start: 0.8338 (t0) cc_final: 0.8039 (t0)
REVERT: A  293 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8208 (mtp85)
  outliers start: 7
  outliers final: 6
  residues processed: 60
  average time/residue: 0.0671
  time to fit residues: 5.2625
Evaluate side-chains
  58 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  293 ARG
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  500 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0270
   chunk 11 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
A 361 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.129989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.102815 restraints weight = 4857.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.33
r_work: 0.3037 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.2195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3770  Z= 0.141
  Angle     :  0.535   6.073   5130  Z= 0.265
  Chirality :  0.039   0.143    597
  Planarity :  0.004   0.026    638
  Dihedral  :  6.194  52.542    535
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 21.57 %
    Favored  : 76.65 %
  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 are not related in a simple way.
  whole:  2.23 (0.42), residues: 466
  helix:  1.70 (0.29), residues: 362
  sheet:  0.40 (1.84), residues: 10
  loop :  1.01 (0.78), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  69 
 TYR   0.012   0.001   TYR A 264 
 PHE   0.030   0.001   PHE A 351 
 TRP   0.010   0.001   TRP A  66 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3768)
  covalent geometry    : angle       0.53330 ( 5126)
  SS BOND              : bond        0.00760 (    2)
  SS BOND              : angle       1.75076 (    4)
  hydrogen bonds       : bond        0.03793 (  236)
  hydrogen bonds       : angle       4.02182 (  699)

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

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

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  932 Ramachandran restraints generated.
    466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A  112 ASP cc_start: 0.8356 (t0) cc_final: 0.8054 (t0)
REVERT: A  293 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8224 (mtp85)
  outliers start: 7
  outliers final: 6
  residues processed: 59
  average time/residue: 0.0581
  time to fit residues: 4.4707
Evaluate side-chains
  57 residues out of total 394 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  293 ARG
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  500 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 29 optimal weight:    0.0970
   chunk 13 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
A 361 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.130275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.103469 restraints weight = 4750.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 2.29
r_work: 0.3036 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3770  Z= 0.133
  Angle     :  0.530   6.203   5130  Z= 0.261
  Chirality :  0.039   0.131    597
  Planarity :  0.004   0.026    638
  Dihedral  :  6.197  52.948    535
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 20.81 %
    Favored  : 76.65 %
  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 are not related in a simple way.
  whole:  2.24 (0.42), residues: 466
  helix:  1.71 (0.29), residues: 362
  sheet:  0.14 (1.77), residues: 10
  loop :  1.03 (0.78), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  69 
 TYR   0.011   0.001   TYR A 264 
 PHE   0.029   0.001   PHE A 351 
 TRP   0.011   0.001   TRP A  66 
 HIS   0.002   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3768)
  covalent geometry    : angle       0.52787 ( 5126)
  SS BOND              : bond        0.00728 (    2)
  SS BOND              : angle       1.60523 (    4)
  hydrogen bonds       : bond        0.03715 (  236)
  hydrogen bonds       : angle       4.00834 (  699)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1085.74 seconds
wall clock time: 19 minutes 17.29 seconds (1157.29 seconds total)