Starting phenix.real_space_refine
on Wed Mar 12 10:48:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ug4_42213/03_2025/8ug4_42213.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ug4_42213/03_2025/8ug4_42213.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ug4_42213/03_2025/8ug4_42213.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ug4_42213/03_2025/8ug4_42213.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ug4_42213/03_2025/8ug4_42213.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ug4_42213/03_2025/8ug4_42213.cif"
  }
  resolution = 3.02
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    5182      2.51       5
     N    1270      2.21       5
     O    1298      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7802
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3901
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 486, 3891
          Classifications: {'peptide': 486}
          Link IDs: {'PTRANS': 8, 'TRANS': 477}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 486, 3891
          Classifications: {'peptide': 486}
          Link IDs: {'PTRANS': 8, 'TRANS': 477}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 3975
  Restraints were copied for chains:
    B
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AHIS A 567 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 567 " occ=0.50
    residue:
      pdb=" N  AHIS B 567 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS B 567 " occ=0.50
  Time building chain proxies: 8.93, per 1000 atoms: 1.14
  Number of scatterers: 7802
  At special positions: 0
  Unit cell: (100.43, 92.13, 90.47, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    1298      8.00
     N    1270      7.00
     C    5182      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.84
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1828

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 2 sheets defined
      77.8% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 86
    Processing helix  chain 'A' and resid 93 through 119
    Processing helix  chain 'A' and resid 122 through 136
    Processing helix  chain 'A' and resid 158 through 186
    Processing helix  chain 'A' and resid 190 through 213
      removed outlier: 3.765A  pdb=" N   ILE A 194 " --> pdb=" O   LYS A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 268
      removed outlier: 3.890A  pdb=" N   ALA A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LYS A 252 " --> pdb=" O   LYS A 248 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA A 253 " --> pdb=" O   GLN A 249 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   HIS A 254 " --> pdb=" O   GLU A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 314 through 340
      removed outlier: 3.632A  pdb=" N   PHE A 318 " --> pdb=" O   ASP A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 389
      removed outlier: 3.589A  pdb=" N   PHE A 389 " --> pdb=" O   MET A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 395
    Processing helix  chain 'A' and resid 395 through 425
    Processing helix  chain 'A' and resid 436 through 467
      removed outlier: 4.273A  pdb=" N   GLU A 440 " --> pdb=" O   GLU A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 499
    Processing helix  chain 'A' and resid 504 through 510
    Processing helix  chain 'A' and resid 513 through 535
    Processing helix  chain 'A' and resid 544 through 549
    Processing helix  chain 'A' and resid 563 through 579
    Processing helix  chain 'B' and resid 57 through 86
    Processing helix  chain 'B' and resid 93 through 119
    Processing helix  chain 'B' and resid 122 through 136
    Processing helix  chain 'B' and resid 158 through 186
    Processing helix  chain 'B' and resid 190 through 213
      removed outlier: 3.765A  pdb=" N   ILE B 194 " --> pdb=" O   LYS B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 268
      removed outlier: 3.890A  pdb=" N   ALA B 251 " --> pdb=" O   ALA B 247 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LYS B 252 " --> pdb=" O   LYS B 248 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA B 253 " --> pdb=" O   GLN B 249 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   HIS B 254 " --> pdb=" O   GLU B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 312
    Processing helix  chain 'B' and resid 314 through 340
      removed outlier: 3.632A  pdb=" N   PHE B 318 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 389
      removed outlier: 3.589A  pdb=" N   PHE B 389 " --> pdb=" O   MET B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 395
    Processing helix  chain 'B' and resid 395 through 425
    Processing helix  chain 'B' and resid 436 through 467
      removed outlier: 4.272A  pdb=" N   GLU B 440 " --> pdb=" O   GLU B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 474 through 499
    Processing helix  chain 'B' and resid 504 through 510
    Processing helix  chain 'B' and resid 513 through 535
    Processing helix  chain 'B' and resid 544 through 549
    Processing helix  chain 'B' and resid 563 through 579
    Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 429
    Processing sheet with id=AA2, first strand: chain 'B' and resid 428 through 429

    614 hydrogen bonds defined for protein.
    1820 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: 2.18

  Time building geometry restraints manager: 2.20 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1357
        1.33 -     1.45: 2158
        1.45 -     1.57: 4401
        1.57 -     1.69: 0
        1.69 -     1.81: 82
  Bond restraints: 7998
  Sorted by residual:
  bond pdb=" CA  SER A 396 "
       pdb=" CB  SER A 396 "
    ideal  model  delta    sigma   weight residual
    1.531  1.481  0.049 1.59e-02 3.96e+03 9.65e+00
  bond pdb=" CA  SER B 396 "
       pdb=" CB  SER B 396 "
    ideal  model  delta    sigma   weight residual
    1.531  1.481  0.049 1.59e-02 3.96e+03 9.65e+00
  bond pdb=" N   ILE B 146 "
       pdb=" CA  ILE B 146 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.12e-02 7.97e+03 9.61e+00
  bond pdb=" N   ILE A 146 "
       pdb=" CA  ILE A 146 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.12e-02 7.97e+03 9.59e+00
  bond pdb=" N   VAL B 219 "
       pdb=" CA  VAL B 219 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.89e+00
  ... (remaining 7993 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.35: 10110
        1.35 -     2.70: 551
        2.70 -     4.05: 124
        4.05 -     5.40: 25
        5.40 -     6.75: 8
  Bond angle restraints: 10818
  Sorted by residual:
  angle pdb=" CA BHIS A 567 "
        pdb=" CB BHIS A 567 "
        pdb=" CG BHIS A 567 "
      ideal   model   delta    sigma   weight residual
     113.80  107.05    6.75 1.00e+00 1.00e+00 4.56e+01
  angle pdb=" CA BHIS B 567 "
        pdb=" CB BHIS B 567 "
        pdb=" CG BHIS B 567 "
      ideal   model   delta    sigma   weight residual
     113.80  107.06    6.74 1.00e+00 1.00e+00 4.54e+01
  angle pdb=" N   LEU B 400 "
        pdb=" CA  LEU B 400 "
        pdb=" C   LEU B 400 "
      ideal   model   delta    sigma   weight residual
     111.14  106.86    4.28 1.08e+00 8.57e-01 1.57e+01
  angle pdb=" N   VAL B 437 "
        pdb=" CA  VAL B 437 "
        pdb=" C   VAL B 437 "
      ideal   model   delta    sigma   weight residual
     112.76  107.75    5.01 1.27e+00 6.20e-01 1.55e+01
  angle pdb=" N   LEU A 400 "
        pdb=" CA  LEU A 400 "
        pdb=" C   LEU A 400 "
      ideal   model   delta    sigma   weight residual
     111.14  106.88    4.26 1.08e+00 8.57e-01 1.55e+01
  ... (remaining 10813 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 4105
       17.85 -    35.69: 435
       35.69 -    53.53: 66
       53.53 -    71.38: 12
       71.38 -    89.22: 8
  Dihedral angle restraints: 4626
    sinusoidal: 1784
      harmonic: 2842
  Sorted by residual:
  dihedral pdb=" CD  ARG A 133 "
           pdb=" NE  ARG A 133 "
           pdb=" CZ  ARG A 133 "
           pdb=" NH1 ARG A 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   65.82  -65.82     1      1.00e+01 1.00e-02 5.67e+01
  dihedral pdb=" CD  ARG B 133 "
           pdb=" NE  ARG B 133 "
           pdb=" CZ  ARG B 133 "
           pdb=" NH1 ARG B 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   65.78  -65.78     1      1.00e+01 1.00e-02 5.66e+01
  dihedral pdb=" N   LEU A 306 "
           pdb=" C   LEU A 306 "
           pdb=" CA  LEU A 306 "
           pdb=" CB  LEU A 306 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  113.75    9.05     0      2.50e+00 1.60e-01 1.31e+01
  ... (remaining 4623 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1064
       0.066 -    0.132: 141
       0.132 -    0.198: 35
       0.198 -    0.264: 8
       0.264 -    0.331: 4
  Chirality restraints: 1252
  Sorted by residual:
  chirality pdb=" CA  LEU A 306 "
            pdb=" N   LEU A 306 "
            pdb=" C   LEU A 306 "
            pdb=" CB  LEU A 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.73e+00
  chirality pdb=" CA  LEU B 306 "
            pdb=" N   LEU B 306 "
            pdb=" C   LEU B 306 "
            pdb=" CB  LEU B 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.70e+00
  chirality pdb=" CA  LEU B 400 "
            pdb=" N   LEU B 400 "
            pdb=" C   LEU B 400 "
            pdb=" CB  LEU B 400 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.27 2.00e-01 2.50e+01 1.89e+00
  ... (remaining 1249 not shown)

  Planarity restraints: 1294
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 133 "   -1.003 9.50e-02 1.11e+02   4.49e-01 1.22e+02
        pdb=" NE  ARG A 133 "    0.060 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 133 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 133 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 133 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 133 "   -1.002 9.50e-02 1.11e+02   4.49e-01 1.22e+02
        pdb=" NE  ARG B 133 "    0.060 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 133 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 133 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 133 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA BHIS B 567 "   -0.024 2.00e-02 2.50e+03   4.85e-02 2.35e+01
        pdb=" C  BHIS B 567 "    0.084 2.00e-02 2.50e+03
        pdb=" O  BHIS B 567 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   SER B 568 "   -0.029 2.00e-02 2.50e+03
  ... (remaining 1291 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 875
        2.75 -     3.28: 8130
        3.28 -     3.82: 14096
        3.82 -     4.36: 15823
        4.36 -     4.90: 27639
  Nonbonded interactions: 66563
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 512 "
            pdb=" OH  TYR B 580 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   PRO A 512 "
            pdb=" OH  TYR A 580 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   ILE A  99 "
            pdb=" OG  SER A 103 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   ILE B  99 "
            pdb=" OG  SER B 103 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   ASP A 314 "
            pdb=" OG1 THR A 317 "
     model   vdw
     2.350 3.040
  ... (remaining 66558 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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=0.50 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:             1.730
  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:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     25.540
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
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      :  0.006   0.049   7998  Z= 0.364
  Angle     :  0.726   6.749  10818  Z= 0.505
  Chirality :  0.055   0.331   1252
  Planarity :  0.018   0.449   1294
  Dihedral  : 14.721  89.224   2798
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.27), residues: 962
  helix:  2.10 (0.18), residues: 724
  sheet:  None (None), residues: 0
  loop : -1.70 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 338 
 HIS   0.005   0.001   HIS B 578 
 PHE   0.018   0.001   PHE B 542 
 TYR   0.017   0.002   TYR B 101 
 ARG   0.002   0.000   ARG B 565 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.848 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.7867 (t80) cc_final: 0.7575 (t80)
REVERT: A  436 GLU cc_start: 0.6713 (tp30) cc_final: 0.6420 (tp30)
REVERT: B  181 PHE cc_start: 0.7825 (t80) cc_final: 0.7568 (t80)
REVERT: B  436 GLU cc_start: 0.6691 (tp30) cc_final: 0.6418 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.2257
  time to fit residues: 36.9059
Evaluate side-chains
  101 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   chunk 29 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 87 optimal weight:    0.8980
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A 567 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.137980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.092809 restraints weight = 23080.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 2.90
r_work: 0.2878 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2822
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2822 r_free = 0.2822    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2821 r_free = 0.2821    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2821
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.1099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   7998  Z= 0.237
  Angle     :  0.486   7.730  10818  Z= 0.273
  Chirality :  0.040   0.231   1252
  Planarity :  0.003   0.030   1294
  Dihedral  :  3.545  14.576   1058
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  6.53 %
    Favored  : 92.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.26), residues: 962
  helix:  2.57 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -1.39 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 239 
 HIS   0.003   0.001   HIS A 209 
 PHE   0.012   0.001   PHE A  63 
 TYR   0.018   0.002   TYR A 101 
 ARG   0.002   0.000   ARG A 133 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.871 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8163 (t80) cc_final: 0.7849 (t80)
REVERT: B  181 PHE cc_start: 0.8127 (t80) cc_final: 0.7822 (t80)
REVERT: B  430 ARG cc_start: 0.8353 (ptt90) cc_final: 0.7850 (ptt180)
  outliers start: 6
  outliers final: 4
  residues processed: 113
  average time/residue: 0.2032
  time to fit residues: 31.3569
Evaluate side-chains
  108 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  432 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 64 optimal weight:    7.9990
   chunk 67 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 88 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 46 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3684 r_free = 0.3684 target = 0.139129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.096136 restraints weight = 17056.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 2.53
r_work: 0.2946 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2859
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2859
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   7998  Z= 0.164
  Angle     :  0.442   6.630  10818  Z= 0.249
  Chirality :  0.038   0.180   1252
  Planarity :  0.003   0.032   1294
  Dihedral  :  3.368  12.932   1058
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  8.67 %
    Favored  : 90.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.82 (0.26), residues: 962
  helix:  2.80 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -1.21 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 239 
 HIS   0.002   0.001   HIS A 232 
 PHE   0.010   0.001   PHE A 542 
 TYR   0.015   0.001   TYR A 101 
 ARG   0.004   0.000   ARG A 430 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 1.020 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8121 (t80) cc_final: 0.7868 (t80)
REVERT: A  366 SER cc_start: 0.7844 (m) cc_final: 0.7636 (p)
REVERT: A  430 ARG cc_start: 0.8339 (ptt90) cc_final: 0.7758 (ptt180)
REVERT: A  436 GLU cc_start: 0.6932 (tp30) cc_final: 0.6705 (tp30)
REVERT: B  181 PHE cc_start: 0.8143 (t80) cc_final: 0.7878 (t80)
REVERT: B  430 ARG cc_start: 0.8308 (ptt90) cc_final: 0.7842 (ptt180)
REVERT: B  436 GLU cc_start: 0.6909 (tp30) cc_final: 0.6703 (tp30)
  outliers start: 9
  outliers final: 4
  residues processed: 112
  average time/residue: 0.1935
  time to fit residues: 30.2502
Evaluate side-chains
  107 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  432 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 57 optimal weight:    0.0470
   chunk 40 optimal weight:    0.0980
   chunk 33 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 64 optimal weight:    0.0060
   chunk 76 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.0298

-------------------------------------------------------------------------------
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 = 0.3684 r_free = 0.3684 target = 0.139218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.093792 restraints weight = 23865.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 2.96
r_work: 0.2913 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2806
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2806 r_free = 0.2806    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2806 r_free = 0.2806    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2806
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   7998  Z= 0.179
  Angle     :  0.426   4.314  10818  Z= 0.243
  Chirality :  0.037   0.159   1252
  Planarity :  0.003   0.033   1294
  Dihedral  :  3.355  14.125   1058
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  8.91 %
    Favored  : 89.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.86 (0.26), residues: 962
  helix:  2.81 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -1.13 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 239 
 HIS   0.002   0.001   HIS B 232 
 PHE   0.010   0.001   PHE A  63 
 TYR   0.017   0.001   TYR B 101 
 ARG   0.004   0.000   ARG A 430 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.801 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8088 (t80) cc_final: 0.7846 (t80)
REVERT: A  430 ARG cc_start: 0.8407 (ptt90) cc_final: 0.7805 (ptt180)
REVERT: A  436 GLU cc_start: 0.6949 (tp30) cc_final: 0.6745 (tp30)
REVERT: B  181 PHE cc_start: 0.8126 (t80) cc_final: 0.7887 (t80)
REVERT: B  430 ARG cc_start: 0.8393 (ptt90) cc_final: 0.7882 (ptt180)
REVERT: B  436 GLU cc_start: 0.7010 (tp30) cc_final: 0.6787 (tp30)
  outliers start: 10
  outliers final: 4
  residues processed: 108
  average time/residue: 0.1972
  time to fit residues: 29.1000
Evaluate side-chains
  104 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  539 SER
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  539 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 78 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 81 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 56 optimal weight:    9.9990
   chunk 68 optimal weight:    5.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
B 261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.135880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.090797 restraints weight = 25843.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 3.00
r_work: 0.2860 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2754
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2754 r_free = 0.2754    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2754 r_free = 0.2754    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2754
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   7998  Z= 0.253
  Angle     :  0.464   4.711  10818  Z= 0.263
  Chirality :  0.039   0.145   1252
  Planarity :  0.003   0.035   1294
  Dihedral  :  3.507  15.194   1058
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  9.62 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.26), residues: 962
  helix:  2.61 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -1.14 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 239 
 HIS   0.003   0.001   HIS A 209 
 PHE   0.012   0.001   PHE A  63 
 TYR   0.019   0.002   TYR A 453 
 ARG   0.003   0.000   ARG A 430 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.836 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8170 (t80) cc_final: 0.7945 (t80)
REVERT: A  436 GLU cc_start: 0.6976 (tp30) cc_final: 0.6734 (tp30)
REVERT: B  181 PHE cc_start: 0.8169 (t80) cc_final: 0.7938 (t80)
REVERT: B  260 LYS cc_start: 0.7114 (mmtt) cc_final: 0.6750 (mmmt)
REVERT: B  261 GLN cc_start: 0.7244 (mm-40) cc_final: 0.7005 (mm-40)
REVERT: B  430 ARG cc_start: 0.8469 (ptt90) cc_final: 0.7883 (ptt180)
REVERT: B  436 GLU cc_start: 0.6968 (tp30) cc_final: 0.6738 (tp30)
  outliers start: 11
  outliers final: 6
  residues processed: 106
  average time/residue: 0.1983
  time to fit residues: 29.0198
Evaluate side-chains
  103 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  539 SER
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  539 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 62 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 71 optimal weight:    0.7980
   chunk 77 optimal weight:    9.9990
   chunk 91 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0270
   overall best weight:    1.0840

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.138866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.094821 restraints weight = 16972.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 2.56
r_work: 0.2933 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2836
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2836 r_free = 0.2836    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2836
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   7998  Z= 0.184
  Angle     :  0.424   4.830  10818  Z= 0.241
  Chirality :  0.037   0.128   1252
  Planarity :  0.003   0.034   1294
  Dihedral  :  3.407  15.534   1058
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.10 %
    Favored  : 89.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.84 (0.26), residues: 962
  helix:  2.74 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -0.95 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 338 
 HIS   0.002   0.001   HIS A 209 
 PHE   0.010   0.001   PHE A  63 
 TYR   0.016   0.001   TYR A 101 
 ARG   0.003   0.000   ARG A 430 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.811 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8117 (t80) cc_final: 0.7910 (t80)
REVERT: A  261 GLN cc_start: 0.7263 (mm-40) cc_final: 0.7024 (mm-40)
REVERT: B  181 PHE cc_start: 0.8116 (t80) cc_final: 0.7900 (t80)
REVERT: B  260 LYS cc_start: 0.7073 (mmtt) cc_final: 0.6762 (mmmt)
REVERT: B  430 ARG cc_start: 0.8389 (ptt90) cc_final: 0.7880 (ptt180)
  outliers start: 6
  outliers final: 5
  residues processed: 103
  average time/residue: 0.2011
  time to fit residues: 28.5011
Evaluate side-chains
  104 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 ILE
Chi-restraints excluded: chain A residue  539 SER
Chi-restraints excluded: chain B residue  217 ILE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  539 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   chunk 88 optimal weight:    4.9990
   chunk 90 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 69 optimal weight:    9.9990
   chunk 62 optimal weight:    7.9990
   chunk 3 optimal weight:    0.6980
   chunk 73 optimal weight:    0.0770
   chunk 82 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
B 261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.140155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.095797 restraints weight = 22828.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 2.85
r_work: 0.2906 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.1791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7998  Z= 0.139
  Angle     :  0.402   5.003  10818  Z= 0.228
  Chirality :  0.036   0.119   1252
  Planarity :  0.003   0.035   1294
  Dihedral  :  3.328  15.768   1058
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.86 %
    Favored  : 89.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.08 (0.26), residues: 962
  helix:  2.90 (0.18), residues: 724
  sheet:  None (None), residues: 0
  loop : -0.84 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 338 
 HIS   0.002   0.000   HIS A 232 
 PHE   0.009   0.001   PHE B 493 
 TYR   0.015   0.001   TYR B 101 
 ARG   0.003   0.000   ARG A 430 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.824 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8116 (t80) cc_final: 0.7889 (t80)
REVERT: A  366 SER cc_start: 0.7879 (m) cc_final: 0.7609 (p)
REVERT: A  430 ARG cc_start: 0.8371 (ptt90) cc_final: 0.7782 (ptt180)
REVERT: B  181 PHE cc_start: 0.8105 (t80) cc_final: 0.7864 (t80)
REVERT: B  260 LYS cc_start: 0.7025 (mmtt) cc_final: 0.6730 (mmmt)
REVERT: B  261 GLN cc_start: 0.7279 (mm-40) cc_final: 0.7000 (mm-40)
REVERT: B  430 ARG cc_start: 0.8360 (ptt90) cc_final: 0.7843 (ptt180)
  outliers start: 7
  outliers final: 5
  residues processed: 108
  average time/residue: 0.1998
  time to fit residues: 29.7236
Evaluate side-chains
  106 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  432 HIS
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  432 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 68 optimal weight:   10.0000
   chunk 71 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 87 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 92 optimal weight:    8.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.139614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.100548 restraints weight = 27316.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 4.17
r_work: 0.2853 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2743
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2743 r_free = 0.2743    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2743 r_free = 0.2743    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2743
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7998  Z= 0.165
  Angle     :  0.419   4.719  10818  Z= 0.238
  Chirality :  0.037   0.125   1252
  Planarity :  0.003   0.035   1294
  Dihedral  :  3.359  16.871   1058
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 10.10 %
    Favored  : 88.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.06 (0.26), residues: 962
  helix:  2.90 (0.18), residues: 724
  sheet:  None (None), residues: 0
  loop : -0.88 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 239 
 HIS   0.002   0.001   HIS A 232 
 PHE   0.010   0.001   PHE A  63 
 TYR   0.016   0.001   TYR A 101 
 ARG   0.003   0.000   ARG A 430 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.809 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8167 (t80) cc_final: 0.7933 (t80)
REVERT: A  260 LYS cc_start: 0.7068 (mmtt) cc_final: 0.6771 (mmmt)
REVERT: A  261 GLN cc_start: 0.7277 (mm-40) cc_final: 0.7072 (mm-40)
REVERT: B  181 PHE cc_start: 0.8170 (t80) cc_final: 0.7926 (t80)
REVERT: B  260 LYS cc_start: 0.7071 (mmtt) cc_final: 0.6780 (mmmt)
REVERT: B  261 GLN cc_start: 0.7257 (mm-40) cc_final: 0.7012 (mm-40)
REVERT: B  430 ARG cc_start: 0.8516 (ptt90) cc_final: 0.7934 (ptt180)
  outliers start: 10
  outliers final: 7
  residues processed: 101
  average time/residue: 0.2007
  time to fit residues: 27.8444
Evaluate side-chains
  103 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  539 SER
Chi-restraints excluded: chain B residue   91 THR
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  266 TYR
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  539 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 66 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   chunk 81 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3690 r_free = 0.3690 target = 0.139864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.099944 restraints weight = 25750.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 3.94
r_work: 0.2840 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2759
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2759
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7998  Z= 0.164
  Angle     :  0.417   5.159  10818  Z= 0.237
  Chirality :  0.037   0.124   1252
  Planarity :  0.003   0.035   1294
  Dihedral  :  3.354  17.353   1058
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 10.69 %
    Favored  : 88.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.08 (0.26), residues: 962
  helix:  2.91 (0.18), residues: 724
  sheet:  None (None), residues: 0
  loop : -0.89 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 422 
 HIS   0.002   0.001   HIS A 209 
 PHE   0.010   0.001   PHE A  63 
 TYR   0.016   0.001   TYR A 101 
 ARG   0.003   0.000   ARG A 430 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.927 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8157 (t80) cc_final: 0.7925 (t80)
REVERT: A  260 LYS cc_start: 0.7006 (mmtt) cc_final: 0.6719 (mmmt)
REVERT: B  181 PHE cc_start: 0.8164 (t80) cc_final: 0.7918 (t80)
REVERT: B  261 GLN cc_start: 0.7281 (mm-40) cc_final: 0.7037 (mm-40)
REVERT: B  430 ARG cc_start: 0.8505 (ptt90) cc_final: 0.7910 (ptt180)
  outliers start: 5
  outliers final: 4
  residues processed: 100
  average time/residue: 0.2429
  time to fit residues: 33.1629
Evaluate side-chains
  99 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  539 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   chunk 64 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.139396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.093365 restraints weight = 35523.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 3.41
r_work: 0.2852 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2794
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2794 r_free = 0.2794    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2794 r_free = 0.2794    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2794
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7998  Z= 0.161
  Angle     :  0.417   5.155  10818  Z= 0.236
  Chirality :  0.037   0.124   1252
  Planarity :  0.003   0.035   1294
  Dihedral  :  3.344  17.480   1058
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 10.81 %
    Favored  : 88.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.10 (0.26), residues: 962
  helix:  2.93 (0.18), residues: 724
  sheet:  None (None), residues: 0
  loop : -0.90 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 338 
 HIS   0.002   0.001   HIS A 232 
 PHE   0.009   0.001   PHE A  63 
 TYR   0.016   0.001   TYR A 101 
 ARG   0.003   0.000   ARG A 430 

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

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

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1924 Ramachandran restraints generated.
    962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 1.825 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8133 (t80) cc_final: 0.7906 (t80)
REVERT: A  260 LYS cc_start: 0.7061 (mmtt) cc_final: 0.6779 (mmmt)
REVERT: A  261 GLN cc_start: 0.7279 (mm-40) cc_final: 0.7075 (mm-40)
REVERT: B  181 PHE cc_start: 0.8141 (t80) cc_final: 0.7898 (t80)
REVERT: B  261 GLN cc_start: 0.7282 (mm-40) cc_final: 0.7041 (mm-40)
REVERT: B  430 ARG cc_start: 0.8452 (ptt90) cc_final: 0.7875 (ptt180)
  outliers start: 5
  outliers final: 5
  residues processed: 99
  average time/residue: 0.3278
  time to fit residues: 44.6776
Evaluate side-chains
  99 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  539 SER
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  539 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0000
   chunk 62 optimal weight:    5.9990
   chunk 45 optimal weight:    0.0370
   chunk 42 optimal weight:    0.2980
   chunk 63 optimal weight:    0.7980
   chunk 79 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.4062

-------------------------------------------------------------------------------
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 = 0.3710 r_free = 0.3710 target = 0.141253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.102593 restraints weight = 25814.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 3.76
r_work: 0.2892 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8559
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7998  Z= 0.123
  Angle     :  0.398   5.386  10818  Z= 0.225
  Chirality :  0.036   0.118   1252
  Planarity :  0.003   0.034   1294
  Dihedral  :  3.269  17.268   1058
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 10.81 %
    Favored  : 88.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.30 (0.27), residues: 962
  helix:  3.08 (0.18), residues: 724
  sheet:  None (None), residues: 0
  loop : -0.83 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 338 
 HIS   0.001   0.000   HIS A 434 
 PHE   0.009   0.001   PHE B 493 
 TYR   0.014   0.001   TYR A 101 
 ARG   0.002   0.000   ARG A 430 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4804.38 seconds
wall clock time: 85 minutes 22.41 seconds (5122.41 seconds total)