Starting phenix.real_space_refine
on Fri Aug 22 13:41:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gof_34177/08_2025/8gof_34177.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gof_34177/08_2025/8gof_34177.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gof_34177/08_2025/8gof_34177.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gof_34177/08_2025/8gof_34177.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gof_34177/08_2025/8gof_34177.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gof_34177/08_2025/8gof_34177.map"
  }
  resolution = 3.0
  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=   0.005
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      10      5.16       5
     C    2192      2.51       5
     N     545      2.21       5
     O     552      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3299
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3268
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 14, 'TRANS': 392}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'LYA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.14, per 1000 atoms: 0.35
  Number of scatterers: 3299
  At special positions: 0
  Unit cell: (80, 72, 66, 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      10     16.00
     O     552      8.00
     N     545      7.00
     C    2192      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: 0.29
  Conformation dependent library (CDL) restraints added in 124.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  770

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 0 sheets defined
      83.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 39
      removed outlier: 3.520A  pdb=" N   CYS A  30 " --> pdb=" O   ARG A  26 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   TYR A  31 " --> pdb=" O   HIS A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 53
    Processing helix  chain 'A' and resid 60 through 68
      removed outlier: 3.517A  pdb=" N   ASN A  66 " --> pdb=" O   GLU A  62 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE A  68 " --> pdb=" O   VAL A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 79
      removed outlier: 3.716A  pdb=" N   TYR A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 90
      removed outlier: 4.241A  pdb=" N   ASP A  88 " --> pdb=" O   PHE A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 113
      removed outlier: 3.524A  pdb=" N   PHE A 103 " --> pdb=" O   GLN A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 132
      removed outlier: 3.517A  pdb=" N   THR A 129 " --> pdb=" O   PHE A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 144
      removed outlier: 4.402A  pdb=" N   SER A 137 " --> pdb=" O   ARG A 133 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   TYR A 139 " --> pdb=" O   ALA A 135 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   PHE A 141 " --> pdb=" O   SER A 137 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   SER A 142 " --> pdb=" O   SER A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 176
      removed outlier: 3.667A  pdb=" N   VAL A 152 " --> pdb=" O   ARG A 148 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   SER A 168 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   VAL A 175 " --> pdb=" O   GLY A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 202
      removed outlier: 3.827A  pdb=" N   PHE A 202 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 263
      removed outlier: 3.886A  pdb=" N   ASP A 260 " --> pdb=" O   ARG A 256 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ARG A 263 " --> pdb=" O   GLY A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 277
    Processing helix  chain 'A' and resid 278 through 296
      removed outlier: 3.558A  pdb=" N   TYR A 287 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   HIS A 289 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 5.210A  pdb=" N   ILE A 290 " --> pdb=" O   TYR A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 304
    Processing helix  chain 'A' and resid 305 through 324
      removed outlier: 3.698A  pdb=" N   THR A 314 " --> pdb=" O   ASP A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 327
      No H-bonds generated for 'chain 'A' and resid 325 through 327'
    Processing helix  chain 'A' and resid 329 through 333
      removed outlier: 3.889A  pdb=" N   ALA A 332 " --> pdb=" O   ILE A 329 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   ARG A 333 " --> pdb=" O   ARG A 330 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 329 through 333'
    Processing helix  chain 'A' and resid 335 through 355
      removed outlier: 3.549A  pdb=" N   THR A 345 " --> pdb=" O   GLY A 341 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   VAL A 350 " --> pdb=" O   GLN A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 360
      No H-bonds generated for 'chain 'A' and resid 358 through 360'
    Processing helix  chain 'A' and resid 361 through 388
      removed outlier: 3.534A  pdb=" N   PHE A 369 " --> pdb=" O   CYS A 365 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   PHE A 372 " --> pdb=" O   ALA A 368 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LEU A 379 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
      Proline residue:  A 381  - end of helix
    Processing helix  chain 'A' and resid 392 through 418
      removed outlier: 3.520A  pdb=" N   ALA A 397 " --> pdb=" O   LYS A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 453
      removed outlier: 3.504A  pdb=" N   GLN A 433 " --> pdb=" O   ARG A 429 " (cutoff:3.500A)

    220 hydrogen bonds defined for protein.
    654 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: 0.51

  Time building geometry restraints manager: 0.37 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: 987
        1.34 -     1.46: 765
        1.46 -     1.57: 1623
        1.57 -     1.69: 0
        1.69 -     1.81: 16
  Bond restraints: 3391
  Sorted by residual:
  bond pdb=" N   MET A 130 "
       pdb=" CA  MET A 130 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.29e-02 6.01e+03 5.04e+00
  bond pdb=" C12 LYA A 601 "
       pdb=" N11 LYA A 601 "
    ideal  model  delta    sigma   weight residual
    1.340  1.370 -0.030 2.00e-02 2.50e+03 2.20e+00
  bond pdb=" C10 LYA A 601 "
       pdb=" N11 LYA A 601 "
    ideal  model  delta    sigma   weight residual
    1.384  1.355  0.029 2.00e-02 2.50e+03 2.16e+00
  bond pdb=" C   VAL A  81 "
       pdb=" O   VAL A  81 "
    ideal  model  delta    sigma   weight residual
    1.240  1.223  0.017 1.26e-02 6.30e+03 1.82e+00
  bond pdb=" C17 LYA A 601 "
       pdb=" N16 LYA A 601 "
    ideal  model  delta    sigma   weight residual
    1.305  1.331 -0.026 2.00e-02 2.50e+03 1.72e+00
  ... (remaining 3386 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 4424
        1.62 -     3.24: 153
        3.24 -     4.86: 32
        4.86 -     6.48: 8
        6.48 -     8.10: 5
  Bond angle restraints: 4622
  Sorted by residual:
  angle pdb=" N   PHE A 103 "
        pdb=" CA  PHE A 103 "
        pdb=" C   PHE A 103 "
      ideal   model   delta    sigma   weight residual
     111.40  105.48    5.92 1.22e+00 6.72e-01 2.35e+01
  angle pdb=" C   TYR A  92 "
        pdb=" CA  TYR A  92 "
        pdb=" CB  TYR A  92 "
      ideal   model   delta    sigma   weight residual
     110.42  102.32    8.10 1.99e+00 2.53e-01 1.66e+01
  angle pdb=" N   LEU A 162 "
        pdb=" CA  LEU A 162 "
        pdb=" C   LEU A 162 "
      ideal   model   delta    sigma   weight residual
     112.23  107.69    4.54 1.26e+00 6.30e-01 1.30e+01
  angle pdb=" N   ILE A 329 "
        pdb=" CA  ILE A 329 "
        pdb=" C   ILE A 329 "
      ideal   model   delta    sigma   weight residual
     112.96  109.62    3.34 1.00e+00 1.00e+00 1.12e+01
  angle pdb=" N   VAL A 428 "
        pdb=" CA  VAL A 428 "
        pdb=" C   VAL A 428 "
      ideal   model   delta    sigma   weight residual
     111.17  115.69   -4.52 1.38e+00 5.25e-01 1.07e+01
  ... (remaining 4617 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.07: 1772
       16.07 -    32.13: 132
       32.13 -    48.19: 31
       48.19 -    64.26: 11
       64.26 -    80.32: 2
  Dihedral angle restraints: 1948
    sinusoidal: 750
      harmonic: 1198
  Sorted by residual:
  dihedral pdb=" CA  ARG A  91 "
           pdb=" C   ARG A  91 "
           pdb=" N   TYR A  92 "
           pdb=" CA  TYR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.19   25.81     0      5.00e+00 4.00e-02 2.66e+01
  dihedral pdb=" CB  ARG A 373 "
           pdb=" CG  ARG A 373 "
           pdb=" CD  ARG A 373 "
           pdb=" NE  ARG A 373 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  118.74  -58.74     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" CA  VAL A 418 "
           pdb=" C   VAL A 418 "
           pdb=" N   SER A 419 "
           pdb=" CA  SER A 419 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.62  -15.38     0      5.00e+00 4.00e-02 9.46e+00
  ... (remaining 1945 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 343
       0.041 -    0.081: 157
       0.081 -    0.122: 26
       0.122 -    0.163: 7
       0.163 -    0.203: 1
  Chirality restraints: 534
  Sorted by residual:
  chirality pdb=" CA  ARG A  42 "
            pdb=" N   ARG A  42 "
            pdb=" C   ARG A  42 "
            pdb=" CB  ARG A  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CB  VAL A 288 "
            pdb=" CA  VAL A 288 "
            pdb=" CG1 VAL A 288 "
            pdb=" CG2 VAL A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.37e-01
  chirality pdb=" CA  LYS A  57 "
            pdb=" N   LYS A  57 "
            pdb=" C   LYS A  57 "
            pdb=" CB  LYS A  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.88e-01
  ... (remaining 531 not shown)

  Planarity restraints: 559
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C20 LYA A 601 "   -0.041 2.00e-02 2.50e+03   1.04e-01 1.36e+02
        pdb=" C23 LYA A 601 "    0.127 2.00e-02 2.50e+03
        pdb=" C4  LYA A 601 "    0.097 2.00e-02 2.50e+03
        pdb=" N22 LYA A 601 "   -0.163 2.00e-02 2.50e+03
        pdb=" O21 LYA A 601 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  69 "    0.044 5.00e-02 4.00e+02   6.50e-02 6.75e+00
        pdb=" N   PRO A  70 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A  70 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A  70 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  41 "    0.011 2.00e-02 2.50e+03   2.23e-02 4.96e+00
        pdb=" C   ILE A  41 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ILE A  41 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ARG A  42 "    0.013 2.00e-02 2.50e+03
  ... (remaining 556 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 986
        2.79 -     3.32: 2929
        3.32 -     3.85: 5651
        3.85 -     4.37: 7087
        4.37 -     4.90: 11655
  Nonbonded interactions: 28308
  Sorted by model distance:
  nonbonded pdb=" O   VAL A  83 "
            pdb=" OG1 THR A  87 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OD1 ASP A  88 "
            pdb=" OH  TYR A  92 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" O   VAL A 304 "
            pdb=" OH  TYR A 366 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   LEU A  32 "
            pdb=" OH  TYR A 136 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   VAL A 380 "
            pdb=" OG1 THR A 384 "
     model   vdw
     2.324 3.040
  ... (remaining 28303 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:             2.040
  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:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.430
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
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   0.056   3391  Z= 0.272
  Angle     :  0.799   8.103   4622  Z= 0.453
  Chirality :  0.046   0.203    534
  Planarity :  0.007   0.104    559
  Dihedral  : 13.255  80.321   1178
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -6.52 (0.22), residues: 403
  helix: -4.45 (0.11), residues: 322
  sheet:  None (None), residues: 0
  loop : -2.16 (0.54), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 133 
 TYR   0.011   0.002   TYR A  92 
 PHE   0.016   0.002   PHE A  37 
 TRP   0.010   0.002   TRP A 107 
 HIS   0.002   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00628 ( 3391)
  covalent geometry    : angle       0.79892 ( 4622)
  hydrogen bonds       : bond        0.27801 (  220)
  hydrogen bonds       : angle      11.32589 (  654)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A   60 THR cc_start: 0.8565 (m) cc_final: 0.8328 (p)
REVERT: A  277 ASN cc_start: 0.8309 (t0) cc_final: 0.7975 (t160)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.7130
  time to fit residues: 30.0250
Evaluate side-chains
  29 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
A 293 ASN
A 346 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.099974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.084124 restraints weight = 4238.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 1.63
r_work: 0.2772 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2640 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3391  Z= 0.164
  Angle     :  0.557   5.941   4622  Z= 0.296
  Chirality :  0.039   0.130    534
  Planarity :  0.005   0.040    559
  Dihedral  :  7.651  85.812    469
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 11.11 %
    Favored  : 87.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.67 (0.34), residues: 403
  helix: -1.65 (0.23), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.36 (0.60), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 303 
 TYR   0.014   0.001   TYR A  35 
 PHE   0.011   0.001   PHE A 372 
 TRP   0.016   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 3391)
  covalent geometry    : angle       0.55713 ( 4622)
  hydrogen bonds       : bond        0.04281 (  220)
  hydrogen bonds       : angle       4.82929 (  654)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A   88 ASP cc_start: 0.8158 (m-30) cc_final: 0.7927 (m-30)
REVERT: A  127 SER cc_start: 0.8847 (m) cc_final: 0.8558 (p)
REVERT: A  204 LYS cc_start: 0.7856 (tttm) cc_final: 0.7484 (tttm)
  outliers start: 4
  outliers final: 0
  residues processed: 40
  average time/residue: 0.5834
  time to fit residues: 24.0235
Evaluate side-chains
  35 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 34 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 7 optimal weight:    0.3980
   chunk 28 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0870
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
A  66 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.102516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.086783 restraints weight = 4095.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 1.60
r_work: 0.2816 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2684 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3391  Z= 0.119
  Angle     :  0.472   5.397   4622  Z= 0.250
  Chirality :  0.037   0.116    534
  Planarity :  0.004   0.030    559
  Dihedral  :  7.122  87.769    469
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.82 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.39), residues: 403
  helix:  0.12 (0.27), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.02 (0.60), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 303 
 TYR   0.010   0.001   TYR A  35 
 PHE   0.012   0.001   PHE A 372 
 TRP   0.011   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 457 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 3391)
  covalent geometry    : angle       0.47199 ( 4622)
  hydrogen bonds       : bond        0.03553 (  220)
  hydrogen bonds       : angle       4.09714 (  654)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A  127 SER cc_start: 0.8830 (m) cc_final: 0.8589 (p)
REVERT: A  251 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7234 (mm)
REVERT: A  293 ASN cc_start: 0.8697 (t0) cc_final: 0.8358 (t160)
  outliers start: 7
  outliers final: 0
  residues processed: 37
  average time/residue: 0.5810
  time to fit residues: 22.1463
Evaluate side-chains
  32 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0370
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.6060

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.103540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.087429 restraints weight = 4111.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.2948 rms_B_bonded: 1.65
r_work: 0.2829 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2692 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3391  Z= 0.134
  Angle     :  0.474   5.397   4622  Z= 0.249
  Chirality :  0.038   0.129    534
  Planarity :  0.003   0.028    559
  Dihedral  :  6.675  81.153    469
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 13.11 %
    Favored  : 84.90 %
  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 aren not related in a simple way.
  whole:  0.72 (0.41), residues: 403
  helix:  0.89 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -0.86 (0.61), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 303 
 TYR   0.012   0.001   TYR A  35 
 PHE   0.011   0.001   PHE A 372 
 TRP   0.011   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3391)
  covalent geometry    : angle       0.47436 ( 4622)
  hydrogen bonds       : bond        0.03531 (  220)
  hydrogen bonds       : angle       3.95631 (  654)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A  162 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7469 (tt)
REVERT: A  251 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7164 (mm)
  outliers start: 7
  outliers final: 1
  residues processed: 35
  average time/residue: 0.6388
  time to fit residues: 23.0244
Evaluate side-chains
  34 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  251 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 30 optimal weight:    0.3980
   chunk 2 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3167 r_free = 0.3167 target = 0.103955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.087905 restraints weight = 4152.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 1.65
r_work: 0.2836 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2700 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3391  Z= 0.129
  Angle     :  0.467   5.357   4622  Z= 0.244
  Chirality :  0.038   0.126    534
  Planarity :  0.003   0.027    559
  Dihedral  :  6.397  75.637    469
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 12.82 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.42), residues: 403
  helix:  1.22 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop : -0.86 (0.61), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 303 
 TYR   0.011   0.001   TYR A  35 
 PHE   0.011   0.001   PHE A 372 
 TRP   0.012   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3391)
  covalent geometry    : angle       0.46656 ( 4622)
  hydrogen bonds       : bond        0.03450 (  220)
  hydrogen bonds       : angle       3.84579 (  654)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 29
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A  162 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7565 (tt)
REVERT: A  251 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7241 (mm)
  outliers start: 9
  outliers final: 2
  residues processed: 36
  average time/residue: 0.5914
  time to fit residues: 21.8351
Evaluate side-chains
  34 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 30
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  251 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 12 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   chunk 34 optimal weight:    0.1980
   chunk 26 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.104309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.088682 restraints weight = 4080.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 1.56
r_work: 0.2850 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3391  Z= 0.121
  Angle     :  0.459   5.347   4622  Z= 0.241
  Chirality :  0.037   0.125    534
  Planarity :  0.003   0.027    559
  Dihedral  :  6.207  70.980    469
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 13.11 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.42), residues: 403
  helix:  1.45 (0.30), residues: 320
  sheet:  None (None), residues: 0
  loop : -0.79 (0.61), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 303 
 TYR   0.010   0.001   TYR A  35 
 PHE   0.011   0.001   PHE A 372 
 TRP   0.011   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3391)
  covalent geometry    : angle       0.45924 ( 4622)
  hydrogen bonds       : bond        0.03383 (  220)
  hydrogen bonds       : angle       3.75945 (  654)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A  162 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7420 (tt)
REVERT: A  251 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7183 (mm)
REVERT: A  298 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8789 (t)
REVERT: A  303 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7913 (ttp80)
  outliers start: 9
  outliers final: 3
  residues processed: 41
  average time/residue: 0.6223
  time to fit residues: 26.2432
Evaluate side-chains
  36 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 LEU
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  298 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.3146 r_free = 0.3146 target = 0.102468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.086548 restraints weight = 4149.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 1.65
r_work: 0.2809 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2673 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3391  Z= 0.158
  Angle     :  0.487   5.370   4622  Z= 0.253
  Chirality :  0.039   0.132    534
  Planarity :  0.003   0.028    559
  Dihedral  :  6.537  78.012    469
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.81 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.42), residues: 403
  helix:  1.49 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.78 (0.62), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 303 
 TYR   0.013   0.001   TYR A  35 
 PHE   0.010   0.001   PHE A 372 
 TRP   0.012   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 3391)
  covalent geometry    : angle       0.48708 ( 4622)
  hydrogen bonds       : bond        0.03559 (  220)
  hydrogen bonds       : angle       3.85007 (  654)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.088 
Fit side-chains
REVERT: A  204 LYS cc_start: 0.8025 (tttm) cc_final: 0.7602 (tttm)
REVERT: A  319 ILE cc_start: 0.7761 (mt) cc_final: 0.7501 (mp)
  outliers start: 7
  outliers final: 1
  residues processed: 40
  average time/residue: 0.6220
  time to fit residues: 25.5735
Evaluate side-chains
  33 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 32
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 18 optimal weight:    0.4980
   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 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.112903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.097381 restraints weight = 4050.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 1.57
r_work: 0.2833 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2700 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3391  Z= 0.138
  Angle     :  0.474   5.354   4622  Z= 0.247
  Chirality :  0.038   0.127    534
  Planarity :  0.003   0.028    559
  Dihedral  :  6.567  79.025    469
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 13.96 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.70 (0.42), residues: 403
  helix:  1.62 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.75 (0.62), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 133 
 TYR   0.011   0.001   TYR A  35 
 PHE   0.010   0.001   PHE A 372 
 TRP   0.012   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3391)
  covalent geometry    : angle       0.47410 ( 4622)
  hydrogen bonds       : bond        0.03471 (  220)
  hydrogen bonds       : angle       3.79497 (  654)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A  204 LYS cc_start: 0.7975 (tttm) cc_final: 0.7548 (tttm)
REVERT: A  319 ILE cc_start: 0.7711 (mt) cc_final: 0.7439 (mp)
  outliers start: 7
  outliers final: 3
  residues processed: 39
  average time/residue: 0.5887
  time to fit residues: 23.5985
Evaluate side-chains
  34 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  442 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.102196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.086239 restraints weight = 4159.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 1.65
r_work: 0.2807 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2672 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3391  Z= 0.161
  Angle     :  0.492   5.375   4622  Z= 0.255
  Chirality :  0.039   0.132    534
  Planarity :  0.003   0.028    559
  Dihedral  :  6.754  82.126    469
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 15.38 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.42), residues: 403
  helix:  1.63 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.72 (0.62), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  61 
 TYR   0.012   0.001   TYR A  35 
 PHE   0.010   0.001   PHE A 372 
 TRP   0.012   0.001   TRP A 107 
 HIS   0.003   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 3391)
  covalent geometry    : angle       0.49157 ( 4622)
  hydrogen bonds       : bond        0.03569 (  220)
  hydrogen bonds       : angle       3.85993 (  654)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A  204 LYS cc_start: 0.8032 (tttm) cc_final: 0.7602 (tttm)
REVERT: A  319 ILE cc_start: 0.7786 (mt) cc_final: 0.7502 (mp)
  outliers start: 4
  outliers final: 3
  residues processed: 34
  average time/residue: 0.6474
  time to fit residues: 22.6373
Evaluate side-chains
  34 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  442 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.103437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.087380 restraints weight = 4088.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 1.65
r_work: 0.2824 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2688 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3391  Z= 0.134
  Angle     :  0.472   5.340   4622  Z= 0.246
  Chirality :  0.038   0.126    534
  Planarity :  0.003   0.028    559
  Dihedral  :  6.674  81.562    469
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 15.95 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.42), residues: 403
  helix:  1.72 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.70 (0.63), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 133 
 TYR   0.011   0.001   TYR A  35 
 PHE   0.010   0.001   PHE A 372 
 TRP   0.011   0.001   TRP A 107 
 HIS   0.002   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3391)
  covalent geometry    : angle       0.47152 ( 4622)
  hydrogen bonds       : bond        0.03449 (  220)
  hydrogen bonds       : angle       3.77877 (  654)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 30
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A  319 ILE cc_start: 0.7760 (mt) cc_final: 0.7480 (mp)
  outliers start: 4
  outliers final: 3
  residues processed: 33
  average time/residue: 0.6225
  time to fit residues: 21.1269
Evaluate side-chains
  33 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  442 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.102732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.086550 restraints weight = 4168.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 1.67
r_work: 0.2807 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2672 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3391  Z= 0.153
  Angle     :  0.484   5.360   4622  Z= 0.252
  Chirality :  0.039   0.130    534
  Planarity :  0.003   0.028    559
  Dihedral  :  6.778  83.256    469
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 15.67 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.42), residues: 403
  helix:  1.69 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.68 (0.63), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 133 
 TYR   0.012   0.001   TYR A  35 
 PHE   0.010   0.001   PHE A 372 
 TRP   0.012   0.001   TRP A 107 
 HIS   0.003   0.000   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 3391)
  covalent geometry    : angle       0.48400 ( 4622)
  hydrogen bonds       : bond        0.03534 (  220)
  hydrogen bonds       : angle       3.82790 (  654)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1162.33 seconds
wall clock time: 20 minutes 36.68 seconds (1236.68 seconds total)