Starting phenix.real_space_refine
on Fri Aug 22 14:06:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sdu_40352/08_2025/8sdu_40352.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sdu_40352/08_2025/8sdu_40352.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sdu_40352/08_2025/8sdu_40352.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sdu_40352/08_2025/8sdu_40352.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sdu_40352/08_2025/8sdu_40352.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sdu_40352/08_2025/8sdu_40352.cif"
  }
  resolution = 2.05
  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=   0.008 sd=   0.092
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      30      5.16       5
     C    2520      2.51       5
     N     653      2.21       5
     O     739      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 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: 3942
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3872
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 500, 3872
          Classifications: {'peptide': 500}
          Link IDs: {'PTRANS': 26, 'TRANS': 473}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 70
          Classifications: {'water': 70}
          Link IDs: {None: 69}
  Time building chain proxies: 1.01, per 1000 atoms: 0.26
  Number of scatterers: 3942
  At special positions: 0
  Unit cell: (76.9133, 68.6133, 97.9399, 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      30     16.00
     O     739      8.00
     N     653      7.00
     C    2520      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.38
  Conformation dependent library (CDL) restraints added in 169.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  928

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 2 sheets defined
      81.0% alpha, 1.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 10
      removed outlier: 3.559A  pdb=" N   LEU A   6 " --> pdb=" O   ALA A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 26
    Processing helix  chain 'A' and resid 27 through 36
      removed outlier: 4.059A  pdb=" N   ALA A  32 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   SER A  33 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 42
    Processing helix  chain 'A' and resid 119 through 125
    Processing helix  chain 'A' and resid 127 through 130
    Processing helix  chain 'A' and resid 131 through 160
      removed outlier: 4.185A  pdb=" N   GLN A 135 " --> pdb=" O   ARG A 131 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ASP A 157 " --> pdb=" O   GLY A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 181
    Processing helix  chain 'A' and resid 184 through 213
      removed outlier: 3.640A  pdb=" N   MET A 207 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 217
      removed outlier: 6.055A  pdb=" N   HIS A 217 " --> pdb=" O   MET A 214 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 214 through 217'
    Processing helix  chain 'A' and resid 218 through 244
      removed outlier: 3.613A  pdb=" N   VAL A 222 " --> pdb=" O   THR A 218 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLY A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   PHE A 235 " --> pdb=" O   SER A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 256
    Processing helix  chain 'A' and resid 256 through 266
      removed outlier: 3.936A  pdb=" N   ILE A 260 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   TRP A 266 " --> pdb=" O   PHE A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 278
    Processing helix  chain 'A' and resid 280 through 296
    Processing helix  chain 'A' and resid 297 through 303
    Processing helix  chain 'A' and resid 305 through 313
    Processing helix  chain 'A' and resid 327 through 332
    Processing helix  chain 'A' and resid 332 through 358
      removed outlier: 3.914A  pdb=" N   LEU A 338 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 364
      removed outlier: 3.600A  pdb=" N   PHE A 363 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   GLY A 364 " --> pdb=" O   GLN A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 392
      removed outlier: 3.866A  pdb=" N   ASP A 378 " --> pdb=" O   PHE A 374 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   LEU A 379 " --> pdb=" O   GLY A 375 " (cutoff:3.500A)
      Proline residue:  A 380  - end of helix
    Processing helix  chain 'A' and resid 393 through 415
      removed outlier: 3.520A  pdb=" N   ILE A 414 " --> pdb=" O   LEU A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 449
      removed outlier: 3.650A  pdb=" N   LEU A 443 " --> pdb=" O   ASN A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 477
      Proline residue:  A 473  - end of helix
    Processing helix  chain 'A' and resid 478 through 481
    Processing helix  chain 'A' and resid 484 through 501
      Proline residue:  A 494  - end of helix
    Processing helix  chain 'A' and resid 502 through 504
      No H-bonds generated for 'chain 'A' and resid 502 through 504'
    Processing helix  chain 'A' and resid 515 through 524
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49
    Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81

    274 hydrogen bonds defined for protein.
    810 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: 0.48

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1215
        1.34 -     1.46: 935
        1.46 -     1.58: 1767
        1.58 -     1.70: 0
        1.70 -     1.81: 47
  Bond restraints: 3964
  Sorted by residual:
  bond pdb=" CB  ARG A 158 "
       pdb=" CG  ARG A 158 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.05e+00
  bond pdb=" CA  ALA A  26 "
       pdb=" C   ALA A  26 "
    ideal  model  delta    sigma   weight residual
    1.522  1.534 -0.013 1.29e-02 6.01e+03 9.97e-01
  bond pdb=" C   PRO A  27 "
       pdb=" O   PRO A  27 "
    ideal  model  delta    sigma   weight residual
    1.237  1.249 -0.012 1.32e-02 5.74e+03 8.45e-01
  bond pdb=" N   PRO A  27 "
       pdb=" CA  PRO A  27 "
    ideal  model  delta    sigma   weight residual
    1.471  1.482 -0.012 1.32e-02 5.74e+03 7.83e-01
  bond pdb=" CA  PRO A  27 "
       pdb=" C   PRO A  27 "
    ideal  model  delta    sigma   weight residual
    1.516  1.530 -0.014 1.75e-02 3.27e+03 6.37e-01
  ... (remaining 3959 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 5296
        1.41 -     2.82: 73
        2.82 -     4.23: 12
        4.23 -     5.64: 10
        5.64 -     7.06: 2
  Bond angle restraints: 5393
  Sorted by residual:
  angle pdb=" CA  TYR A 264 "
        pdb=" CB  TYR A 264 "
        pdb=" CG  TYR A 264 "
      ideal   model   delta    sigma   weight residual
     113.90  119.07   -5.17 1.80e+00 3.09e-01 8.26e+00
  angle pdb=" CA  ARG A 158 "
        pdb=" CB  ARG A 158 "
        pdb=" CG  ARG A 158 "
      ideal   model   delta    sigma   weight residual
     114.10  119.51   -5.41 2.00e+00 2.50e-01 7.31e+00
  angle pdb=" CB  ARG A 158 "
        pdb=" CG  ARG A 158 "
        pdb=" CD  ARG A 158 "
      ideal   model   delta    sigma   weight residual
     111.30  117.20   -5.90 2.30e+00 1.89e-01 6.58e+00
  angle pdb=" N   VAL A 256 "
        pdb=" CA  VAL A 256 "
        pdb=" C   VAL A 256 "
      ideal   model   delta    sigma   weight residual
     108.88  114.27   -5.39 2.16e+00 2.14e-01 6.23e+00
  angle pdb=" CA  VAL A 256 "
        pdb=" C   VAL A 256 "
        pdb=" N   PRO A 257 "
      ideal   model   delta    sigma   weight residual
     118.88  121.99   -3.11 1.54e+00 4.22e-01 4.08e+00
  ... (remaining 5388 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 2091
       17.89 -    35.78: 204
       35.78 -    53.67: 40
       53.67 -    71.56: 9
       71.56 -    89.44: 3
  Dihedral angle restraints: 2347
    sinusoidal: 904
      harmonic: 1443
  Sorted by residual:
  dihedral pdb=" CB  GLU A 270 "
           pdb=" CG  GLU A 270 "
           pdb=" CD  GLU A 270 "
           pdb=" OE1 GLU A 270 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.70   88.70     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CA  CYS A  49 "
           pdb=" CB  CYS A  49 "
           pdb=" SG  CYS A  49 "
           pdb=" SG  CYS A 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00  -19.30  -53.70     1      2.00e+01 2.50e-03 9.79e+00
  dihedral pdb=" CG  LYS A 382 "
           pdb=" CD  LYS A 382 "
           pdb=" CE  LYS A 382 "
           pdb=" NZ  LYS A 382 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.09   57.09     3      1.50e+01 4.44e-03 9.43e+00
  ... (remaining 2344 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 398
       0.027 -    0.055: 148
       0.055 -    0.082: 55
       0.082 -    0.110: 25
       0.110 -    0.137: 5
  Chirality restraints: 631
  Sorted by residual:
  chirality pdb=" CA  ILE A 415 "
            pdb=" N   ILE A 415 "
            pdb=" C   ILE A 415 "
            pdb=" CB  ILE A 415 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.70e-01
  chirality pdb=" CA  TYR A 264 "
            pdb=" N   TYR A 264 "
            pdb=" C   TYR A 264 "
            pdb=" CB  TYR A 264 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 3.98e-01
  chirality pdb=" CA  VAL A 110 "
            pdb=" N   VAL A 110 "
            pdb=" C   VAL A 110 "
            pdb=" CB  VAL A 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.64e-01
  ... (remaining 628 not shown)

  Planarity restraints: 671
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 103 "   -0.030 5.00e-02 4.00e+02   4.58e-02 3.36e+00
        pdb=" N   PRO A 104 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 104 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 104 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  26 "   -0.022 5.00e-02 4.00e+02   3.37e-02 1.81e+00
        pdb=" N   PRO A  27 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A  27 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  27 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 244 "   -0.022 5.00e-02 4.00e+02   3.35e-02 1.79e+00
        pdb=" N   PRO A 245 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 245 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 245 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 668 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 733
        2.76 -     3.30: 4114
        3.30 -     3.83: 7456
        3.83 -     4.37: 8554
        4.37 -     4.90: 14073
  Nonbonded interactions: 34930
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 444 "
            pdb=" O   PRO A 505 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OH  TYR A 230 "
            pdb=" O   HOH A 601 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   LEU A  28 "
            pdb=" O   HOH A 602 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   HOH A 603 "
            pdb=" O   HOH A 656 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OG  SER A 118 "
            pdb=" O   HOH A 603 "
     model   vdw
     2.254 3.040
  ... (remaining 34925 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:             1.310
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.640
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:8.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
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      :  0.002   0.031   3966  Z= 0.109
  Angle     :  0.490   7.056   5397  Z= 0.249
  Chirality :  0.037   0.137    631
  Planarity :  0.004   0.046    671
  Dihedral  : 14.855  89.444   1413
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 13.57 %
    Favored  : 85.71 %
  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:  2.05 (0.38), residues: 492
  helix:  1.37 (0.26), residues: 368
  sheet: -0.05 (1.59), residues: 10
  loop :  1.90 (0.68), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.017   0.001   TYR A 264 
 PHE   0.012   0.001   PHE A  16 
 TRP   0.015   0.002   TRP A 274 
 HIS   0.004   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 3964)
  covalent geometry    : angle       0.48962 ( 5393)
  SS BOND              : bond        0.00294 (    2)
  SS BOND              : angle       1.09390 (    4)
  hydrogen bonds       : bond        0.20739 (  274)
  hydrogen bonds       : angle       6.81527 (  810)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A  300 GLU cc_start: 0.7221 (mp0) cc_final: 0.7004 (mp0)
  outliers start: 3
  outliers final: 2
  residues processed: 68
  average time/residue: 0.7020
  time to fit residues: 49.0375
Evaluate side-chains
  63 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  278 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.2980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0670
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A   9 GLN
A 205 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.183266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.148933 restraints weight = 2893.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 0.84
r_work: 0.3362 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3966  Z= 0.140
  Angle     :  0.525   6.944   5397  Z= 0.278
  Chirality :  0.038   0.130    631
  Planarity :  0.004   0.036    671
  Dihedral  :  3.718  14.824    544
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 12.86 %
    Favored  : 86.43 %
  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:  2.71 (0.38), residues: 492
  helix:  1.95 (0.27), residues: 375
  sheet:  0.03 (1.65), residues: 10
  loop :  1.70 (0.67), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 134 
 TYR   0.017   0.001   TYR A 264 
 PHE   0.014   0.001   PHE A 351 
 TRP   0.013   0.002   TRP A 346 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 3964)
  covalent geometry    : angle       0.52471 ( 5393)
  SS BOND              : bond        0.00306 (    2)
  SS BOND              : angle       0.91622 (    4)
  hydrogen bonds       : bond        0.06033 (  274)
  hydrogen bonds       : angle       4.92286 (  810)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 66
  time to evaluate  : 0.152 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 67
  average time/residue: 0.6244
  time to fit residues: 43.1057
Evaluate side-chains
  58 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  327 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 29 optimal weight:    0.4980
   chunk 16 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0010
   chunk 36 optimal weight:    9.9990
   chunk 1 optimal weight:    0.5980
   chunk 35 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
A 205 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.185250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.151125 restraints weight = 2834.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 0.85
r_work: 0.3374 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3966  Z= 0.123
  Angle     :  0.478   6.631   5397  Z= 0.254
  Chirality :  0.037   0.122    631
  Planarity :  0.004   0.027    671
  Dihedral  :  3.597  13.908    542
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.62 %
    Favored  : 85.71 %
  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:  2.83 (0.39), residues: 492
  helix:  2.08 (0.27), residues: 375
  sheet:  0.34 (1.70), residues: 10
  loop :  1.52 (0.66), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.018   0.001   TYR A 264 
 PHE   0.013   0.001   PHE A 351 
 TRP   0.010   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 3964)
  covalent geometry    : angle       0.47781 ( 5393)
  SS BOND              : bond        0.00287 (    2)
  SS BOND              : angle       0.84316 (    4)
  hydrogen bonds       : bond        0.05392 (  274)
  hydrogen bonds       : angle       4.60402 (  810)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  103 GLU cc_start: 0.7829 (pt0) cc_final: 0.7615 (pt0)
  outliers start: 7
  outliers final: 1
  residues processed: 61
  average time/residue: 0.6055
  time to fit residues: 38.0801
Evaluate side-chains
  63 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 34 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 45 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   chunk 14 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A 205 ASN
A 419 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.178722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.143613 restraints weight = 2802.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 0.83
r_work: 0.3281 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 2.87 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.1127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3966  Z= 0.188
  Angle     :  0.575   6.899   5397  Z= 0.313
  Chirality :  0.041   0.144    631
  Planarity :  0.005   0.034    671
  Dihedral  :  3.872  14.774    542
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.67 %
    Favored  : 86.90 %
  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:  2.64 (0.38), residues: 492
  helix:  1.85 (0.26), residues: 371
  sheet: -0.13 (1.61), residues: 10
  loop :  1.93 (0.65), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 134 
 TYR   0.024   0.002   TYR A 264 
 PHE   0.018   0.002   PHE A  40 
 TRP   0.012   0.002   TRP A 274 
 HIS   0.007   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 3964)
  covalent geometry    : angle       0.57419 ( 5393)
  SS BOND              : bond        0.00407 (    2)
  SS BOND              : angle       1.21216 (    4)
  hydrogen bonds       : bond        0.07123 (  274)
  hydrogen bonds       : angle       5.01834 (  810)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.163 
Fit side-chains
  outliers start: 6
  outliers final: 1
  residues processed: 61
  average time/residue: 0.6012
  time to fit residues: 37.7578
Evaluate side-chains
  59 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   chunk 4 optimal weight:    0.0270
   chunk 38 optimal weight:    0.0770
   chunk 27 optimal weight:    9.9990
   chunk 24 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A   9 GLN
A 205 ASN
A 419 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.182540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.148537 restraints weight = 2858.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 0.91
r_work: 0.3329 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.1364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3966  Z= 0.129
  Angle     :  0.493   6.721   5397  Z= 0.263
  Chirality :  0.037   0.128    631
  Planarity :  0.004   0.027    671
  Dihedral  :  3.683  14.212    542
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.90 %
    Favored  : 86.43 %
  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:  2.84 (0.39), residues: 492
  helix:  2.07 (0.27), residues: 374
  sheet:  0.19 (1.64), residues: 10
  loop :  1.66 (0.66), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.019   0.001   TYR A 264 
 PHE   0.015   0.001   PHE A 386 
 TRP   0.010   0.001   TRP A 274 
 HIS   0.004   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 3964)
  covalent geometry    : angle       0.49237 ( 5393)
  SS BOND              : bond        0.00263 (    2)
  SS BOND              : angle       1.03696 (    4)
  hydrogen bonds       : bond        0.05578 (  274)
  hydrogen bonds       : angle       4.66892 (  810)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.161 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 68
  average time/residue: 0.6667
  time to fit residues: 46.6543
Evaluate side-chains
  65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 LYS
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  391 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 30 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 35 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 39 optimal weight:    9.9990
   chunk 16 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A 205 ASN
A 419 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.179745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.144880 restraints weight = 2844.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 0.84
r_work: 0.3298 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 2.80 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.1178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3966  Z= 0.172
  Angle     :  0.555   6.805   5397  Z= 0.299
  Chirality :  0.040   0.142    631
  Planarity :  0.004   0.033    671
  Dihedral  :  3.835  14.362    542
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.38 %
    Favored  : 85.71 %
  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:  2.69 (0.38), residues: 492
  helix:  1.89 (0.26), residues: 371
  sheet:  0.07 (1.59), residues: 10
  loop :  1.88 (0.65), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.023   0.002   TYR A 264 
 PHE   0.015   0.002   PHE A  16 
 TRP   0.012   0.002   TRP A 274 
 HIS   0.006   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3964)
  covalent geometry    : angle       0.55399 ( 5393)
  SS BOND              : bond        0.00386 (    2)
  SS BOND              : angle       1.21211 (    4)
  hydrogen bonds       : bond        0.06753 (  274)
  hydrogen bonds       : angle       4.92131 (  810)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.171 
Fit side-chains
  outliers start: 8
  outliers final: 6
  residues processed: 67
  average time/residue: 0.6124
  time to fit residues: 42.3160
Evaluate side-chains
  69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  297 LYS
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  391 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 35 optimal weight:    0.0980
   chunk 15 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 3 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.2188

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A   9 GLN
A 205 ASN
A 419 HIS
A 439 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.181562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.147172 restraints weight = 2911.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 0.89
r_work: 0.3318 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3966  Z= 0.143
  Angle     :  0.519   6.743   5397  Z= 0.277
  Chirality :  0.038   0.133    631
  Planarity :  0.004   0.030    671
  Dihedral  :  3.755  14.294    542
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 12.62 %
    Favored  : 85.95 %
  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:  2.70 (0.38), residues: 492
  helix:  1.95 (0.26), residues: 374
  sheet:  0.31 (1.59), residues: 10
  loop :  1.64 (0.65), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.020   0.001   TYR A 264 
 PHE   0.015   0.002   PHE A 386 
 TRP   0.012   0.002   TRP A 274 
 HIS   0.004   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 3964)
  covalent geometry    : angle       0.51869 ( 5393)
  SS BOND              : bond        0.00326 (    2)
  SS BOND              : angle       1.07655 (    4)
  hydrogen bonds       : bond        0.06052 (  274)
  hydrogen bonds       : angle       4.76945 (  810)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  417 LYS cc_start: 0.7957 (mmtm) cc_final: 0.7574 (mmmt)
  outliers start: 6
  outliers final: 3
  residues processed: 66
  average time/residue: 0.6739
  time to fit residues: 45.7776
Evaluate side-chains
  65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  297 LYS
Chi-restraints excluded: chain A residue  337 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 48 optimal weight:   50.0000
   chunk 21 optimal weight:   10.0000
   chunk 12 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 7 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A 205 ASN
A 419 HIS
A 439 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.181846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.147334 restraints weight = 2845.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 0.84
r_work: 0.3333 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.1330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3966  Z= 0.144
  Angle     :  0.522   6.726   5397  Z= 0.278
  Chirality :  0.038   0.135    631
  Planarity :  0.004   0.030    671
  Dihedral  :  3.751  14.265    542
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.62 %
    Favored  : 85.71 %
  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:  2.69 (0.38), residues: 492
  helix:  1.95 (0.26), residues: 374
  sheet:  0.33 (1.60), residues: 10
  loop :  1.62 (0.66), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.021   0.002   TYR A 264 
 PHE   0.015   0.002   PHE A 386 
 TRP   0.012   0.002   TRP A 274 
 HIS   0.005   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 3964)
  covalent geometry    : angle       0.52093 ( 5393)
  SS BOND              : bond        0.00333 (    2)
  SS BOND              : angle       1.08322 (    4)
  hydrogen bonds       : bond        0.06062 (  274)
  hydrogen bonds       : angle       4.76184 (  810)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.101 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 67
  average time/residue: 0.6215
  time to fit residues: 42.8685
Evaluate side-chains
  68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  297 LYS
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  391 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 46 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 48 optimal weight:   50.0000
   chunk 49 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A 205 ASN
A 419 HIS
A 439 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.180581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.145932 restraints weight = 2893.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 0.89
r_work: 0.3296 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3966  Z= 0.160
  Angle     :  0.545   6.792   5397  Z= 0.292
  Chirality :  0.039   0.141    631
  Planarity :  0.004   0.031    671
  Dihedral  :  3.815  14.383    542
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 12.62 %
    Favored  : 85.48 %
  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:  2.68 (0.38), residues: 492
  helix:  1.90 (0.26), residues: 371
  sheet:  0.19 (1.57), residues: 10
  loop :  1.81 (0.65), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.022   0.002   TYR A 264 
 PHE   0.015   0.002   PHE A 386 
 TRP   0.012   0.002   TRP A 274 
 HIS   0.006   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3964)
  covalent geometry    : angle       0.54392 ( 5393)
  SS BOND              : bond        0.00363 (    2)
  SS BOND              : angle       1.11981 (    4)
  hydrogen bonds       : bond        0.06489 (  274)
  hydrogen bonds       : angle       4.86270 (  810)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.158 
Fit side-chains
  outliers start: 8
  outliers final: 6
  residues processed: 67
  average time/residue: 0.6884
  time to fit residues: 47.4534
Evaluate side-chains
  68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  297 LYS
Chi-restraints excluded: chain A residue  337 HIS
Chi-restraints excluded: chain A residue  391 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 39 optimal weight:    7.9990
   chunk 2 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0570
   chunk 13 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0770
   chunk 33 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0570
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.3174

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A 205 ASN
A 419 HIS
A 439 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.186312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.152508 restraints weight = 2913.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 0.95
r_work: 0.3363 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3966  Z= 0.118
  Angle     :  0.492   6.602   5397  Z= 0.255
  Chirality :  0.037   0.125    631
  Planarity :  0.004   0.027    671
  Dihedral  :  3.570  14.229    542
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 13.33 %
    Favored  : 85.71 %
  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:  2.91 (0.39), residues: 492
  helix:  2.20 (0.27), residues: 375
  sheet:  0.44 (1.68), residues: 10
  loop :  1.30 (0.65), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.018   0.001   TYR A 264 
 PHE   0.016   0.001   PHE A 386 
 TRP   0.011   0.001   TRP A 346 
 HIS   0.002   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 3964)
  covalent geometry    : angle       0.49144 ( 5393)
  SS BOND              : bond        0.00265 (    2)
  SS BOND              : angle       0.88405 (    4)
  hydrogen bonds       : bond        0.04793 (  274)
  hydrogen bonds       : angle       4.45559 (  810)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.158 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 65
  average time/residue: 0.6718
  time to fit residues: 45.0002
Evaluate side-chains
  61 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 59
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  297 LYS
Chi-restraints excluded: chain A residue  337 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 4 optimal weight:    0.4980
   chunk 27 optimal weight:    8.9990
   chunk 18 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 5 optimal weight:    0.2980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A 205 ASN
A 419 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.185300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.151157 restraints weight = 2866.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 0.85
r_work: 0.3366 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3966  Z= 0.125
  Angle     :  0.504   6.488   5397  Z= 0.261
  Chirality :  0.037   0.125    631
  Planarity :  0.004   0.027    671
  Dihedral  :  3.587  14.084    542
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 14.05 %
    Favored  : 85.00 %
  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:  2.91 (0.39), residues: 492
  helix:  2.16 (0.27), residues: 374
  sheet:  0.28 (1.63), residues: 10
  loop :  1.49 (0.65), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.018   0.001   TYR A 264 
 PHE   0.017   0.002   PHE A 386 
 TRP   0.012   0.001   TRP A 346 
 HIS   0.003   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 3964)
  covalent geometry    : angle       0.50374 ( 5393)
  SS BOND              : bond        0.00255 (    2)
  SS BOND              : angle       0.92225 (    4)
  hydrogen bonds       : bond        0.05289 (  274)
  hydrogen bonds       : angle       4.51885 (  810)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2389.50 seconds
wall clock time: 41 minutes 23.69 seconds (2483.69 seconds total)