Starting phenix.real_space_refine
on Fri Aug 22 14:09:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mau_63758/08_2025/9mau_63758_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mau_63758/08_2025/9mau_63758.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mau_63758/08_2025/9mau_63758.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mau_63758/08_2025/9mau_63758.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mau_63758/08_2025/9mau_63758_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mau_63758/08_2025/9mau_63758_neut.cif"
  }
  resolution = 2.87
  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=   0.128
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      31      5.16       5
     C    2511      2.51       5
     N     657      2.21       5
     O     675      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3874
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3874
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 506, 3874
          Classifications: {'peptide': 506}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 26, 'TRANS': 479}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 15
  Time building chain proxies: 1.16, per 1000 atoms: 0.30
  Number of scatterers: 3874
  At special positions: 0
  Unit cell: (105.316, 52.192, 68.968, 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      31     16.00
     O     675      8.00
     N     657      7.00
     C    2511      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=2.01
    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: 0.26
  Conformation dependent library (CDL) restraints added in 162.0 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  932

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 2 sheets defined
      80.8% alpha, 1.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 10
      removed outlier: 3.936A  pdb=" N   GLN A   8 " --> pdb=" O   ASN A   4 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 26
    Processing helix  chain 'A' and resid 28 through 36
      removed outlier: 4.423A  pdb=" N   ALA A  32 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   SER A  33 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 40
    Processing helix  chain 'A' and resid 56 through 61
    Processing helix  chain 'A' and resid 62 through 67
      removed outlier: 4.084A  pdb=" N   TRP A  66 " --> pdb=" O   GLY A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 124
    Processing helix  chain 'A' and resid 127 through 130
    Processing helix  chain 'A' and resid 131 through 160
      removed outlier: 4.326A  pdb=" N   GLN A 135 " --> pdb=" O   ARG A 131 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLN A 138 " --> pdb=" O   ARG A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 181
    Processing helix  chain 'A' and resid 184 through 213
      removed outlier: 3.602A  pdb=" N   MET A 207 " --> pdb=" O   SER A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 217
      No H-bonds generated for 'chain 'A' and resid 215 through 217'
    Processing helix  chain 'A' and resid 218 through 244
      removed outlier: 3.601A  pdb=" N   GLN A 234 " --> pdb=" O   TYR A 230 " (cutoff:3.500A)
      removed outlier: 4.001A  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 265
      removed outlier: 4.067A  pdb=" N   ALA A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 268
      No H-bonds generated for 'chain 'A' and resid 266 through 268'
    Processing helix  chain 'A' and resid 271 through 279
    Processing helix  chain 'A' and resid 280 through 296
    Processing helix  chain 'A' and resid 297 through 304
    Processing helix  chain 'A' and resid 305 through 312
      removed outlier: 3.535A  pdb=" N   ALA A 311 " --> pdb=" O   GLU A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 332
      removed outlier: 3.903A  pdb=" N   LEU A 329 " --> pdb=" O   SER A 325 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 358
      removed outlier: 3.584A  pdb=" N   LEU A 338 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 393
      removed outlier: 3.616A  pdb=" N   ASP A 378 " --> pdb=" O   PHE A 374 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   LEU A 379 " --> pdb=" O   GLY A 375 " (cutoff:3.500A)
      Proline residue:  A 380  - end of helix
      removed outlier: 3.562A  pdb=" N   LEU A 383 " --> pdb=" O   LEU A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 415
      removed outlier: 3.700A  pdb=" N   ALA A 397 " --> pdb=" O   GLY A 393 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLN A 398 " --> pdb=" O   ARG A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 449
      removed outlier: 3.574A  pdb=" N   ARG A 423 " --> pdb=" O   GLN A 419 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   TYR A 449 " --> pdb=" O   THR A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 452
      No H-bonds generated for 'chain 'A' and resid 450 through 452'
    Processing helix  chain 'A' and resid 453 through 477
      Proline residue:  A 473  - end of helix
    Processing helix  chain 'A' and resid 478 through 480
      No H-bonds generated for 'chain 'A' and resid 478 through 480'
    Processing helix  chain 'A' and resid 484 through 501
      Proline residue:  A 494  - end of helix
    Processing helix  chain 'A' and resid 515 through 522
      removed outlier: 3.505A  pdb=" N   LEU A 519 " --> pdb=" O   THR A 515 " (cutoff:3.500A)
    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

    268 hydrogen bonds defined for protein.
    795 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: 0.55

  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:
        1.19 -     1.31: 603
        1.31 -     1.44: 1076
        1.44 -     1.56: 2236
        1.56 -     1.69: 1
        1.69 -     1.81: 49
  Bond restraints: 3965
  Sorted by residual:
  bond pdb=" C   CYS A 128 "
       pdb=" O   CYS A 128 "
    ideal  model  delta    sigma   weight residual
    1.243  1.206  0.038 9.50e-03 1.11e+04 1.57e+01
  bond pdb=" C   SER A 472 "
       pdb=" O   SER A 472 "
    ideal  model  delta    sigma   weight residual
    1.244  1.204  0.039 1.00e-02 1.00e+04 1.54e+01
  bond pdb=" C   THR A 424 "
       pdb=" O   THR A 424 "
    ideal  model  delta    sigma   weight residual
    1.237  1.191  0.045 1.16e-02 7.43e+03 1.52e+01
  bond pdb=" C   PHE A 339 "
       pdb=" O   PHE A 339 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.044 1.15e-02 7.56e+03 1.44e+01
  bond pdb=" C   GLN A  20 "
       pdb=" O   GLN A  20 "
    ideal  model  delta    sigma   weight residual
    1.237  1.193  0.044 1.17e-02 7.31e+03 1.39e+01
  ... (remaining 3960 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 4695
        1.86 -     3.71: 576
        3.71 -     5.57: 90
        5.57 -     7.43: 25
        7.43 -     9.29: 13
  Bond angle restraints: 5399
  Sorted by residual:
  angle pdb=" N   SER A  77 "
        pdb=" CA  SER A  77 "
        pdb=" C   SER A  77 "
      ideal   model   delta    sigma   weight residual
     111.36  118.89   -7.53 1.09e+00 8.42e-01 4.77e+01
  angle pdb=" N   ASN A 412 "
        pdb=" CA  ASN A 412 "
        pdb=" C   ASN A 412 "
      ideal   model   delta    sigma   weight residual
     111.69  103.39    8.30 1.23e+00 6.61e-01 4.55e+01
  angle pdb=" N   ASP A   5 "
        pdb=" CA  ASP A   5 "
        pdb=" C   ASP A   5 "
      ideal   model   delta    sigma   weight residual
     113.41  105.41    8.00 1.22e+00 6.72e-01 4.30e+01
  angle pdb=" N   PHE A 259 "
        pdb=" CA  PHE A 259 "
        pdb=" C   PHE A 259 "
      ideal   model   delta    sigma   weight residual
     112.90  105.03    7.87 1.31e+00 5.83e-01 3.61e+01
  angle pdb=" N   VAL A 143 "
        pdb=" CA  VAL A 143 "
        pdb=" C   VAL A 143 "
      ideal   model   delta    sigma   weight residual
     110.62  104.52    6.10 1.02e+00 9.61e-01 3.58e+01
  ... (remaining 5394 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.59: 2183
       17.59 -    35.17: 129
       35.17 -    52.75: 23
       52.75 -    70.33: 4
       70.33 -    87.91: 3
  Dihedral angle restraints: 2342
    sinusoidal: 891
      harmonic: 1451
  Sorted by residual:
  dihedral pdb=" C   VAL A 164 "
           pdb=" N   VAL A 164 "
           pdb=" CA  VAL A 164 "
           pdb=" CB  VAL A 164 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.58    9.58     0      2.50e+00 1.60e-01 1.47e+01
  dihedral pdb=" C   VAL A 428 "
           pdb=" N   VAL A 428 "
           pdb=" CA  VAL A 428 "
           pdb=" CB  VAL A 428 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.23    8.23     0      2.50e+00 1.60e-01 1.08e+01
  dihedral pdb=" C   PHE A 152 "
           pdb=" N   PHE A 152 "
           pdb=" CA  PHE A 152 "
           pdb=" CB  PHE A 152 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.68    8.08     0      2.50e+00 1.60e-01 1.05e+01
  ... (remaining 2339 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 424
       0.073 -    0.145: 144
       0.145 -    0.218: 49
       0.218 -    0.291: 10
       0.291 -    0.364: 3
  Chirality restraints: 630
  Sorted by residual:
  chirality pdb=" CA  PHE A 152 "
            pdb=" N   PHE A 152 "
            pdb=" C   PHE A 152 "
            pdb=" CB  PHE A 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.31e+00
  chirality pdb=" CA  TYR A 354 "
            pdb=" N   TYR A 354 "
            pdb=" C   TYR A 354 "
            pdb=" CB  TYR A 354 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" CB  VAL A 127 "
            pdb=" CA  VAL A 127 "
            pdb=" CG1 VAL A 127 "
            pdb=" CG2 VAL A 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.26e+00
  ... (remaining 627 not shown)

  Planarity restraints: 679
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  26 "   -0.047 5.00e-02 4.00e+02   7.16e-02 8.21e+00
        pdb=" N   PRO A  27 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO A  27 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A  27 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 493 "   -0.039 5.00e-02 4.00e+02   5.87e-02 5.51e+00
        pdb=" N   PRO A 494 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 494 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 494 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 499 "    0.012 2.00e-02 2.50e+03   2.30e-02 5.29e+00
        pdb=" C   ALA A 499 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ALA A 499 "    0.015 2.00e-02 2.50e+03
        pdb=" N   VAL A 500 "    0.013 2.00e-02 2.50e+03
  ... (remaining 676 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 1531
        2.90 -     3.40: 4037
        3.40 -     3.90: 6783
        3.90 -     4.40: 7911
        4.40 -     4.90: 12542
  Nonbonded interactions: 32804
  Sorted by model distance:
  nonbonded pdb=" N   HIS A  48 "
            pdb=" O   HIS A  48 "
     model   vdw
     2.403 2.496
  nonbonded pdb=" N   THR A 119 "
            pdb=" O   THR A 119 "
     model   vdw
     2.406 2.496
  nonbonded pdb=" N   GLY A  14 "
            pdb=" O   GLY A  14 "
     model   vdw
     2.522 2.496
  nonbonded pdb=" N   ASN A  39 "
            pdb=" N   PHE A  40 "
     model   vdw
     2.548 2.560
  nonbonded pdb=" N   ASP A   5 "
            pdb=" N   LEU A   6 "
     model   vdw
     2.552 2.560
  ... (remaining 32799 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:             0.830
  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:                    0.020
  Process input model:                     5.360
  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:6.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6482
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      :  0.010   0.046   3967  Z= 0.786
  Angle     :  1.386   9.286   5403  Z= 0.937
  Chirality :  0.085   0.364    630
  Planarity :  0.008   0.072    679
  Dihedral  : 12.107  87.915   1404
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  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: -0.76 (0.36), residues: 500
  helix: -0.63 (0.25), residues: 373
  sheet: -0.13 (1.48), residues: 10
  loop :  0.64 (0.56), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 394 
 TYR   0.024   0.003   TYR A 264 
 PHE   0.019   0.003   PHE A 351 
 TRP   0.017   0.002   TRP A 346 
 HIS   0.007   0.002   HIS A 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.01045 ( 3965)
  covalent geometry    : angle       1.38622 ( 5399)
  SS BOND              : bond        0.01679 (    2)
  SS BOND              : angle       1.41856 (    4)
  hydrogen bonds       : bond        0.22378 (  268)
  hydrogen bonds       : angle       8.04680 (  795)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A  286 ARG cc_start: 0.5987 (mtt180) cc_final: 0.5658 (mtm180)
REVERT: A  327 MET cc_start: 0.7010 (mmm) cc_final: 0.5822 (ttp)
REVERT: A  331 ARG cc_start: 0.6445 (ttt180) cc_final: 0.6182 (ttt-90)
REVERT: A  358 MET cc_start: 0.7283 (mmm) cc_final: 0.7038 (mmm)
REVERT: A  415 ILE cc_start: 0.7409 (mt) cc_final: 0.7176 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.5303
  time to fit residues: 46.6252
Evaluate side-chains
  58 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A  38 GLN
A  39 ASN
A 217 HIS
A 417 GLN
A 455 GLN
A 510 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.149384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.111404 restraints weight = 4045.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 2.11
r_work: 0.2974 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2842 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6808
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   3967  Z= 0.166
  Angle     :  0.602   6.157   5403  Z= 0.319
  Chirality :  0.040   0.148    630
  Planarity :  0.006   0.050    679
  Dihedral  :  4.304  16.367    546
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  7.54 %
    Favored  : 91.48 %
  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:  1.37 (0.38), residues: 500
  helix:  1.01 (0.27), residues: 362
  sheet: -0.97 (1.47), residues: 10
  loop :  1.18 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 280 
 TYR   0.023   0.002   TYR A 264 
 PHE   0.015   0.002   PHE A 351 
 TRP   0.011   0.001   TRP A 346 
 HIS   0.004   0.002   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 3965)
  covalent geometry    : angle       0.60105 ( 5399)
  SS BOND              : bond        0.00960 (    2)
  SS BOND              : angle       1.10652 (    4)
  hydrogen bonds       : bond        0.05418 (  268)
  hydrogen bonds       : angle       4.82249 (  795)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A  327 MET cc_start: 0.7324 (mmm) cc_final: 0.6118 (tmt)
REVERT: A  394 ARG cc_start: 0.7814 (tpp-160) cc_final: 0.7578 (mtt90)
REVERT: A  452 MET cc_start: 0.5849 (OUTLIER) cc_final: 0.5433 (ppp)
  outliers start: 4
  outliers final: 1
  residues processed: 50
  average time/residue: 0.5614
  time to fit residues: 29.0310
Evaluate side-chains
  46 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 44
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  452 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0670
   chunk 40 optimal weight:    0.4980
   chunk 46 optimal weight:    0.6980
   chunk 6 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9980
   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   8 GLN
A 455 GLN
A 510 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.149713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.111470 restraints weight = 4002.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3109 rms_B_bonded: 2.10
r_work: 0.2982 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6883
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      :  0.003   0.037   3967  Z= 0.136
  Angle     :  0.540   5.603   5403  Z= 0.276
  Chirality :  0.037   0.128    630
  Planarity :  0.005   0.040    679
  Dihedral  :  4.110  14.002    546
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  :  9.25 %
    Favored  : 88.32 %
  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:  2.04 (0.38), residues: 500
  helix:  1.60 (0.27), residues: 364
  sheet: -1.67 (1.44), residues: 10
  loop :  1.18 (0.61), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 280 
 TYR   0.020   0.002   TYR A 444 
 PHE   0.015   0.001   PHE A 351 
 TRP   0.008   0.001   TRP A 274 
 HIS   0.003   0.001   HIS A  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3965)
  covalent geometry    : angle       0.54015 ( 5399)
  SS BOND              : bond        0.00729 (    2)
  SS BOND              : angle       0.77972 (    4)
  hydrogen bonds       : bond        0.04833 (  268)
  hydrogen bonds       : angle       4.37312 (  795)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A   34 HIS cc_start: 0.8336 (OUTLIER) cc_final: 0.8109 (m-70)
REVERT: A  273 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.5760 (mmp80)
REVERT: A  286 ARG cc_start: 0.6054 (mtt180) cc_final: 0.5692 (mtm180)
REVERT: A  327 MET cc_start: 0.7298 (mmm) cc_final: 0.6048 (tmt)
REVERT: A  331 ARG cc_start: 0.6959 (ttt180) cc_final: 0.6585 (ttp80)
REVERT: A  394 ARG cc_start: 0.7883 (tpp-160) cc_final: 0.7671 (mtt90)
REVERT: A  452 MET cc_start: 0.5746 (ptm) cc_final: 0.5468 (ppp)
  outliers start: 10
  outliers final: 2
  residues processed: 57
  average time/residue: 0.6274
  time to fit residues: 36.8698
Evaluate side-chains
  47 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 43
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 HIS
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  203 SER
Chi-restraints excluded: chain A residue  273 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 30 optimal weight:    8.9990
   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 455 GLN
A 510 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.147158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.108482 restraints weight = 4000.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 2.10
r_work: 0.2945 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2814 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6877
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3967  Z= 0.158
  Angle     :  0.540   5.051   5403  Z= 0.277
  Chirality :  0.039   0.119    630
  Planarity :  0.005   0.038    679
  Dihedral  :  4.011  14.603    546
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.90 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.38), residues: 500
  helix:  1.63 (0.27), residues: 363
  sheet: -2.02 (1.27), residues: 10
  loop :  1.01 (0.60), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 158 
 TYR   0.026   0.002   TYR A 444 
 PHE   0.016   0.002   PHE A 351 
 TRP   0.010   0.001   TRP A 274 
 HIS   0.004   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 3965)
  covalent geometry    : angle       0.54010 ( 5399)
  SS BOND              : bond        0.00787 (    2)
  SS BOND              : angle       0.67299 (    4)
  hydrogen bonds       : bond        0.04701 (  268)
  hydrogen bonds       : angle       4.25100 (  795)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.097 
Fit side-chains
REVERT: A    9 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6757 (tp-100)
REVERT: A  286 ARG cc_start: 0.5967 (mtt180) cc_final: 0.5588 (mtm180)
REVERT: A  327 MET cc_start: 0.7160 (mmm) cc_final: 0.5937 (tmt)
REVERT: A  331 ARG cc_start: 0.7027 (ttt180) cc_final: 0.6629 (ttp80)
REVERT: A  394 ARG cc_start: 0.7861 (tpp-160) cc_final: 0.7589 (mtt90)
REVERT: A  452 MET cc_start: 0.5996 (OUTLIER) cc_final: 0.5674 (ppp)
  outliers start: 7
  outliers final: 2
  residues processed: 53
  average time/residue: 0.5528
  time to fit residues: 30.2488
Evaluate side-chains
  50 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLN
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  452 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0770
   overall best weight:    0.9342

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

Flipped N/Q/H residues before XYZ refinement:
A 455 GLN
A 510 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.144789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.107266 restraints weight = 4028.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 2.06
r_work: 0.2929 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2798 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6963
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3967  Z= 0.163
  Angle     :  0.536   5.185   5403  Z= 0.273
  Chirality :  0.039   0.121    630
  Planarity :  0.005   0.037    679
  Dihedral  :  3.986  14.732    546
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 14.84 %
    Favored  : 83.94 %
  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:  1.88 (0.38), residues: 500
  helix:  1.54 (0.27), residues: 370
  sheet: -2.08 (1.27), residues: 10
  loop :  0.89 (0.61), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 280 
 TYR   0.024   0.002   TYR A 444 
 PHE   0.016   0.002   PHE A 351 
 TRP   0.011   0.001   TRP A 274 
 HIS   0.004   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 3965)
  covalent geometry    : angle       0.53631 ( 5399)
  SS BOND              : bond        0.00762 (    2)
  SS BOND              : angle       0.57607 (    4)
  hydrogen bonds       : bond        0.04700 (  268)
  hydrogen bonds       : angle       4.21303 (  795)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A    9 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6846 (tp-100)
REVERT: A  286 ARG cc_start: 0.5949 (mtt180) cc_final: 0.5572 (mtm180)
REVERT: A  327 MET cc_start: 0.7210 (mmm) cc_final: 0.5984 (tmt)
REVERT: A  331 ARG cc_start: 0.7086 (ttt180) cc_final: 0.6681 (ttp80)
REVERT: A  394 ARG cc_start: 0.7981 (tpp-160) cc_final: 0.7725 (mtt90)
REVERT: A  452 MET cc_start: 0.6188 (ptm) cc_final: 0.5849 (ppp)
  outliers start: 5
  outliers final: 3
  residues processed: 53
  average time/residue: 0.5793
  time to fit residues: 31.7249
Evaluate side-chains
  51 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLN
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  443 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 210 ASN
A 510 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.144604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.107032 restraints weight = 4103.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 2.06
r_work: 0.2926 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2795 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3967  Z= 0.155
  Angle     :  0.523   5.195   5403  Z= 0.266
  Chirality :  0.038   0.118    630
  Planarity :  0.004   0.036    679
  Dihedral  :  3.909  14.659    546
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.11 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.38), residues: 500
  helix:  1.64 (0.27), residues: 370
  sheet: -2.05 (1.23), residues: 10
  loop :  0.85 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 280 
 TYR   0.021   0.002   TYR A 444 
 PHE   0.016   0.002   PHE A 351 
 TRP   0.011   0.001   TRP A 274 
 HIS   0.004   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 3965)
  covalent geometry    : angle       0.52340 ( 5399)
  SS BOND              : bond        0.00712 (    2)
  SS BOND              : angle       0.53675 (    4)
  hydrogen bonds       : bond        0.04576 (  268)
  hydrogen bonds       : angle       4.15081 (  795)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A    9 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6821 (tp-100)
REVERT: A  286 ARG cc_start: 0.5919 (mtt180) cc_final: 0.5562 (mtm180)
REVERT: A  327 MET cc_start: 0.7212 (mmm) cc_final: 0.6017 (tmt)
REVERT: A  331 ARG cc_start: 0.7131 (ttt180) cc_final: 0.6743 (ttp80)
REVERT: A  394 ARG cc_start: 0.7986 (tpp-160) cc_final: 0.7770 (mtt90)
REVERT: A  443 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.6033 (mp)
REVERT: A  444 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.7069 (t80)
REVERT: A  452 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.5852 (ppp)
  outliers start: 10
  outliers final: 3
  residues processed: 54
  average time/residue: 0.4853
  time to fit residues: 27.1366
Evaluate side-chains
  52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLN
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  444 TYR
Chi-restraints excluded: chain A residue  452 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 38 optimal weight:    0.3980
   chunk 23 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 34 optimal weight:    0.3980
   chunk 32 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 455 GLN
A 510 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.149830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.111186 restraints weight = 4037.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 2.20
r_work: 0.2968 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2831 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6823
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3967  Z= 0.129
  Angle     :  0.501   5.247   5403  Z= 0.253
  Chirality :  0.037   0.120    630
  Planarity :  0.004   0.035    679
  Dihedral  :  3.793  14.392    546
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.36 %
    Favored  : 83.70 %
  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:  2.17 (0.38), residues: 500
  helix:  1.80 (0.27), residues: 370
  sheet: -2.04 (1.27), residues: 10
  loop :  0.87 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 158 
 TYR   0.020   0.001   TYR A 264 
 PHE   0.015   0.001   PHE A 351 
 TRP   0.012   0.001   TRP A 274 
 HIS   0.005   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 3965)
  covalent geometry    : angle       0.50087 ( 5399)
  SS BOND              : bond        0.00570 (    2)
  SS BOND              : angle       0.54140 (    4)
  hydrogen bonds       : bond        0.04297 (  268)
  hydrogen bonds       : angle       4.07644 (  795)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.096 
Fit side-chains
REVERT: A    6 LEU cc_start: 0.5226 (OUTLIER) cc_final: 0.4959 (mp)
REVERT: A    9 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6707 (tp-100)
REVERT: A  286 ARG cc_start: 0.5717 (mtt180) cc_final: 0.5379 (mtm180)
REVERT: A  327 MET cc_start: 0.7121 (mmm) cc_final: 0.5893 (tmt)
REVERT: A  331 ARG cc_start: 0.7094 (ttt180) cc_final: 0.6678 (ttp80)
REVERT: A  443 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5832 (mp)
REVERT: A  452 MET cc_start: 0.6008 (ptm) cc_final: 0.5719 (ppp)
  outliers start: 8
  outliers final: 4
  residues processed: 54
  average time/residue: 0.5500
  time to fit residues: 30.7136
Evaluate side-chains
  53 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue    9 GLN
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  443 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 11 optimal weight:    0.1980
   chunk 5 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 510 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.150262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.111615 restraints weight = 3960.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 2.11
r_work: 0.2981 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2846 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6856
moved from start:          0.3246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3967  Z= 0.128
  Angle     :  0.502   5.169   5403  Z= 0.253
  Chirality :  0.037   0.119    630
  Planarity :  0.004   0.034    679
  Dihedral  :  3.755  14.186    546
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 15.33 %
    Favored  : 83.21 %
  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:  2.26 (0.38), residues: 500
  helix:  1.85 (0.27), residues: 370
  sheet: -2.04 (1.29), residues: 10
  loop :  0.94 (0.63), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 394 
 TYR   0.019   0.001   TYR A 264 
 PHE   0.016   0.001   PHE A 351 
 TRP   0.011   0.001   TRP A 274 
 HIS   0.005   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 3965)
  covalent geometry    : angle       0.50210 ( 5399)
  SS BOND              : bond        0.00526 (    2)
  SS BOND              : angle       0.54675 (    4)
  hydrogen bonds       : bond        0.04290 (  268)
  hydrogen bonds       : angle       4.07311 (  795)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A    6 LEU cc_start: 0.5281 (OUTLIER) cc_final: 0.5039 (mp)
REVERT: A    9 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6712 (tp-100)
REVERT: A  286 ARG cc_start: 0.5788 (mtt180) cc_final: 0.5442 (mtm180)
REVERT: A  327 MET cc_start: 0.7282 (mmm) cc_final: 0.6052 (tmt)
REVERT: A  443 LEU cc_start: 0.6372 (OUTLIER) cc_final: 0.5992 (mp)
REVERT: A  452 MET cc_start: 0.6114 (ptm) cc_final: 0.5851 (ppp)
  outliers start: 6
  outliers final: 3
  residues processed: 49
  average time/residue: 0.5429
  time to fit residues: 27.6003
Evaluate side-chains
  49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue    9 GLN
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  443 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   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 455 GLN
A 510 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.149412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.110597 restraints weight = 4017.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 2.18
r_work: 0.2960 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2823 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6864
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3967  Z= 0.137
  Angle     :  0.509   5.372   5403  Z= 0.257
  Chirality :  0.037   0.118    630
  Planarity :  0.004   0.034    679
  Dihedral  :  3.742  14.218    546
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 15.09 %
    Favored  : 82.97 %
  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:  2.18 (0.39), residues: 500
  helix:  1.76 (0.27), residues: 375
  sheet: -2.02 (1.30), residues: 10
  loop :  0.97 (0.65), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 394 
 TYR   0.019   0.001   TYR A 264 
 PHE   0.016   0.001   PHE A 351 
 TRP   0.012   0.001   TRP A 274 
 HIS   0.006   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 3965)
  covalent geometry    : angle       0.50873 ( 5399)
  SS BOND              : bond        0.00575 (    2)
  SS BOND              : angle       0.54221 (    4)
  hydrogen bonds       : bond        0.04352 (  268)
  hydrogen bonds       : angle       4.08518 (  795)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A    9 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6681 (tp-100)
REVERT: A  286 ARG cc_start: 0.5776 (mtt180) cc_final: 0.5434 (mtm180)
REVERT: A  327 MET cc_start: 0.7265 (mmm) cc_final: 0.6054 (tmt)
REVERT: A  443 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.5994 (mp)
REVERT: A  444 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.6887 (t80)
REVERT: A  452 MET cc_start: 0.6102 (ptm) cc_final: 0.5837 (ppp)
  outliers start: 8
  outliers final: 3
  residues processed: 54
  average time/residue: 0.5105
  time to fit residues: 28.6369
Evaluate side-chains
  52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLN
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  444 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0970
   chunk 9 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 47 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 = 0.3733 r_free = 0.3733 target = 0.150629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.111918 restraints weight = 4012.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3108 rms_B_bonded: 2.11
r_work: 0.2980 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6910
moved from start:          0.3346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3967  Z= 0.129
  Angle     :  0.518   6.391   5403  Z= 0.264
  Chirality :  0.038   0.156    630
  Planarity :  0.004   0.034    679
  Dihedral  :  3.741  14.133    546
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 17.03 %
    Favored  : 81.75 %
  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:  2.21 (0.39), residues: 500
  helix:  1.78 (0.27), residues: 375
  sheet: -2.08 (1.30), residues: 10
  loop :  1.00 (0.66), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 394 
 TYR   0.020   0.001   TYR A 264 
 PHE   0.015   0.001   PHE A 351 
 TRP   0.012   0.001   TRP A 274 
 HIS   0.005   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 3965)
  covalent geometry    : angle       0.51840 ( 5399)
  SS BOND              : bond        0.00529 (    2)
  SS BOND              : angle       0.55451 (    4)
  hydrogen bonds       : bond        0.04261 (  268)
  hydrogen bonds       : angle       4.06708 (  795)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A  273 ARG cc_start: 0.6420 (mtp85) cc_final: 0.6083 (mmp80)
REVERT: A  286 ARG cc_start: 0.5810 (mtt180) cc_final: 0.5465 (mtm180)
REVERT: A  327 MET cc_start: 0.7285 (mmm) cc_final: 0.6081 (tmt)
REVERT: A  443 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6071 (mp)
REVERT: A  452 MET cc_start: 0.6115 (ptm) cc_final: 0.5865 (ppp)
  outliers start: 5
  outliers final: 2
  residues processed: 47
  average time/residue: 0.5624
  time to fit residues: 27.4204
Evaluate side-chains
  47 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  330 LEU
Chi-restraints excluded: chain A residue  443 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 47 optimal weight:    0.0570
   chunk 1 optimal weight:    0.3980
   chunk 6 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 39 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
A 455 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.151367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.112365 restraints weight = 3977.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 2.18
r_work: 0.2990 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6863
moved from start:          0.3441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3967  Z= 0.122
  Angle     :  0.509   5.369   5403  Z= 0.259
  Chirality :  0.037   0.149    630
  Planarity :  0.004   0.034    679
  Dihedral  :  3.676  13.991    546
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 16.79 %
    Favored  : 82.00 %
  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:  2.26 (0.39), residues: 500
  helix:  1.81 (0.27), residues: 375
  sheet: -2.16 (1.29), residues: 10
  loop :  1.06 (0.66), residues: 115

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 394 
 TYR   0.020   0.001   TYR A 264 
 PHE   0.015   0.001   PHE A 351 
 TRP   0.012   0.001   TRP A 274 
 HIS   0.005   0.001   HIS A  34 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 3965)
  covalent geometry    : angle       0.50915 ( 5399)
  SS BOND              : bond        0.00535 (    2)
  SS BOND              : angle       0.82691 (    4)
  hydrogen bonds       : bond        0.04158 (  268)
  hydrogen bonds       : angle       4.03776 (  795)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1577.53 seconds
wall clock time: 27 minutes 35.09 seconds (1655.09 seconds total)