Starting phenix.real_space_refine
on Fri Aug 22 15:01:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ont_17000/08_2025/8ont_17000_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ont_17000/08_2025/8ont_17000.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ont_17000/08_2025/8ont_17000_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ont_17000/08_2025/8ont_17000_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ont_17000/08_2025/8ont_17000.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ont_17000/08_2025/8ont_17000.map"
  }
  resolution = 3.66
  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=   0.063
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      26      5.16       5
     C    2831      2.51       5
     N     696      2.21       5
     O     762      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 4316
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 438, 3367
          Classifications: {'peptide': 438}
          Link IDs: {'PTRANS': 16, 'TRANS': 421}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 906
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 43
          Unusual residues: {'PLC': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 1.15, per 1000 atoms: 0.27
  Number of scatterers: 4316
  At special positions: 0
  Unit cell: (75.516, 96.348, 78.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      26     16.00
     P       1     15.00
     O     762      8.00
     N     696      7.00
     C    2831      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 298 " - pdb=" SG  CYS A 311 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " 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: 0.33
  Conformation dependent library (CDL) restraints added in 129.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1034

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 2 sheets defined
      72.2% alpha, 6.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 65
    Processing helix  chain 'A' and resid 66 through 81
    Processing helix  chain 'A' and resid 84 through 110
      removed outlier: 3.546A  pdb=" N   VAL A  88 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 121
      removed outlier: 3.553A  pdb=" N   LEU A 116 " --> pdb=" O   HIS A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 157
      Proline residue:  A 143  - end of helix
    Processing helix  chain 'A' and resid 159 through 181
      removed outlier: 4.672A  pdb=" N   LEU A 172 " --> pdb=" O   VAL A 168 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   LEU A 173 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 208
      removed outlier: 3.684A  pdb=" N   GLU A 186 " --> pdb=" O   ALA A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 219
    Processing helix  chain 'A' and resid 225 through 241
    Processing helix  chain 'A' and resid 242 through 253
      removed outlier: 4.282A  pdb=" N   PHE A 246 " --> pdb=" O   PRO A 242 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ALA A 250 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   VAL A 252 " --> pdb=" O   HIS A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 300
    Processing helix  chain 'A' and resid 304 through 314
      removed outlier: 3.916A  pdb=" N   ASP A 313 " --> pdb=" O   ASN A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 328
      removed outlier: 3.850A  pdb=" N   LEU A 323 " --> pdb=" O   ALA A 319 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   ASN A 325 " --> pdb=" O   MET A 321 " (cutoff:3.500A)
      removed outlier: 5.627A  pdb=" N   VAL A 326 " --> pdb=" O   LEU A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 362
      removed outlier: 4.042A  pdb=" N   VAL A 334 " --> pdb=" O   SER A 330 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   PHE A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ALA A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU A 362 " --> pdb=" O   MET A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 390
      Proline residue:  A 382  - end of helix
    Processing helix  chain 'A' and resid 391 through 423
      Proline residue:  A 411  - end of helix
      Proline residue:  A 416  - end of helix
    Processing helix  chain 'A' and resid 423 through 428
    Processing helix  chain 'A' and resid 433 through 466
      removed outlier: 3.891A  pdb=" N   HIS A 465 " --> pdb=" O   ASP A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 496
    Processing helix  chain 'B' and resid 87 through 91
    Processing helix  chain 'B' and resid 103 through 108
      removed outlier: 3.693A  pdb=" N   ARG B 107 " --> pdb=" O   PHE B 103 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 49
      removed outlier: 6.398A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ALA B  33 " --> pdb=" O   GLY B  99 " (cutoff:3.500A)

    320 hydrogen bonds defined for protein.
    939 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: 0.44

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 658
        1.31 -     1.43: 1199
        1.43 -     1.56: 2509
        1.56 -     1.68: 2
        1.68 -     1.81: 42
  Bond restraints: 4410
  Sorted by residual:
  bond pdb=" CB  PLC A 601 "
       pdb=" O3  PLC A 601 "
    ideal  model  delta    sigma   weight residual
    1.327  1.434 -0.107 2.00e-02 2.50e+03 2.85e+01
  bond pdb=" C'  PLC A 601 "
       pdb=" O2  PLC A 601 "
    ideal  model  delta    sigma   weight residual
    1.332  1.430 -0.098 2.00e-02 2.50e+03 2.40e+01
  bond pdb=" C'  PLC A 601 "
       pdb=" C1' PLC A 601 "
    ideal  model  delta    sigma   weight residual
    1.503  1.569 -0.066 2.00e-02 2.50e+03 1.08e+01
  bond pdb=" O3P PLC A 601 "
       pdb=" P   PLC A 601 "
    ideal  model  delta    sigma   weight residual
    1.634  1.689 -0.055 2.00e-02 2.50e+03 7.50e+00
  bond pdb=" CB  PLC A 601 "
       pdb=" C1B PLC A 601 "
    ideal  model  delta    sigma   weight residual
    1.504  1.556 -0.052 2.00e-02 2.50e+03 6.70e+00
  ... (remaining 4405 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.19: 5947
        3.19 -     6.39: 44
        6.39 -     9.58: 3
        9.58 -    12.77: 1
       12.77 -    15.96: 1
  Bond angle restraints: 5996
  Sorted by residual:
  angle pdb=" O3P PLC A 601 "
        pdb=" P   PLC A 601 "
        pdb=" O4P PLC A 601 "
      ideal   model   delta    sigma   weight residual
      93.62  109.58  -15.96 3.00e+00 1.11e-01 2.83e+01
  angle pdb=" O1P PLC A 601 "
        pdb=" P   PLC A 601 "
        pdb=" O2P PLC A 601 "
      ideal   model   delta    sigma   weight residual
     119.61  109.11   10.50 3.00e+00 1.11e-01 1.22e+01
  angle pdb=" C1' PLC A 601 "
        pdb=" C'  PLC A 601 "
        pdb=" O2  PLC A 601 "
      ideal   model   delta    sigma   weight residual
     111.19  119.79   -8.60 3.00e+00 1.11e-01 8.22e+00
  angle pdb=" C1B PLC A 601 "
        pdb=" CB  PLC A 601 "
        pdb=" O3  PLC A 601 "
      ideal   model   delta    sigma   weight residual
     111.34  119.59   -8.25 3.00e+00 1.11e-01 7.57e+00
  angle pdb=" C   ALA A 300 "
        pdb=" CA  ALA A 300 "
        pdb=" CB  ALA A 300 "
      ideal   model   delta    sigma   weight residual
     110.42  115.43   -5.01 1.99e+00 2.53e-01 6.34e+00
  ... (remaining 5991 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.83: 2315
       20.83 -    41.66: 234
       41.66 -    62.48: 34
       62.48 -    83.31: 5
       83.31 -   104.14: 6
  Dihedral angle restraints: 2594
    sinusoidal: 986
      harmonic: 1608
  Sorted by residual:
  dihedral pdb=" O2  PLC A 601 "
           pdb=" C1  PLC A 601 "
           pdb=" C2  PLC A 601 "
           pdb=" O3P PLC A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -55.71   48.43 -104.14     1      3.00e+01 1.11e-03 1.33e+01
  dihedral pdb=" C3  PLC A 601 "
           pdb=" C1  PLC A 601 "
           pdb=" C2  PLC A 601 "
           pdb=" O3P PLC A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      67.16  168.71 -101.55     1      3.00e+01 1.11e-03 1.28e+01
  dihedral pdb=" C2' PLC A 601 "
           pdb=" C'  PLC A 601 "
           pdb=" C1' PLC A 601 "
           pdb=" O2  PLC A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     169.53   79.09   90.44     1      3.00e+01 1.11e-03 1.07e+01
  ... (remaining 2591 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 576
       0.046 -    0.093: 114
       0.093 -    0.139: 20
       0.139 -    0.185: 0
       0.185 -    0.231: 1
  Chirality restraints: 711
  Sorted by residual:
  chirality pdb=" C2  PLC A 601 "
            pdb=" C1  PLC A 601 "
            pdb=" C3  PLC A 601 "
            pdb=" O2  PLC A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.31   -2.54    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  PRO A 143 "
            pdb=" N   PRO A 143 "
            pdb=" C   PRO A 143 "
            pdb=" CB  PRO A 143 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.00e-01
  chirality pdb=" CA  VAL B  93 "
            pdb=" N   VAL B  93 "
            pdb=" C   VAL B  93 "
            pdb=" CB  VAL B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.69e-01
  ... (remaining 708 not shown)

  Planarity restraints: 733
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  19 "   -0.307 9.50e-02 1.11e+02   1.38e-01 1.17e+01
        pdb=" NE  ARG B  19 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  19 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  19 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  19 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B  87 "    0.022 5.00e-02 4.00e+02   3.38e-02 1.83e+00
        pdb=" N   PRO B  88 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO B  88 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B  88 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 142 "   -0.022 5.00e-02 4.00e+02   3.31e-02 1.75e+00
        pdb=" N   PRO A 143 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 143 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 143 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 730 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 30
        2.51 -     3.10: 3511
        3.10 -     3.70: 6575
        3.70 -     4.30: 8905
        4.30 -     4.90: 15773
  Nonbonded interactions: 34794
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  82 "
            pdb=" OG1 THR A 296 "
     model   vdw
     1.908 3.040
  nonbonded pdb=" O   SER A 139 "
            pdb=" OG  SER A 402 "
     model   vdw
     2.025 3.040
  nonbonded pdb=" O   VAL A 491 "
            pdb=" OG1 THR A 495 "
     model   vdw
     2.071 3.040
  nonbonded pdb=" OD1 ASP A  66 "
            pdb=" OG1 THR A 346 "
     model   vdw
     2.076 3.040
  nonbonded pdb=" OG1 THR A 351 "
            pdb=" ND2 ASN A 372 "
     model   vdw
     2.083 3.120
  ... (remaining 34789 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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 group one per residue
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:             0.390
  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:                     4.830
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.107   4412  Z= 0.267
  Angle     :  0.671  15.964   6000  Z= 0.314
  Chirality :  0.038   0.231    711
  Planarity :  0.006   0.138    733
  Dihedral  : 16.916 104.141   1554
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 33.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 25.22 %
    Favored  : 73.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.38), residues: 552
  helix:  2.54 (0.27), residues: 360
  sheet: -0.03 (0.82), residues: 47
  loop : -2.54 (0.50), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  82 
 TYR   0.017   0.002   TYR B  80 
 PHE   0.014   0.001   PHE A 236 
 TRP   0.006   0.001   TRP A  86 
 HIS   0.003   0.001   HIS A 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00578 ( 4410)
  covalent geometry    : angle       0.67078 ( 5996)
  SS BOND              : bond        0.00071 (    2)
  SS BOND              : angle       0.88138 (    4)
  hydrogen bonds       : bond        0.12325 (  320)
  hydrogen bonds       : angle       6.57836 (  939)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.098 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 54
  average time/residue: 0.0934
  time to fit residues: 6.0058
Evaluate side-chains
  54 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain B residue    6 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0030
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.4980
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
A 299 ASN
A 372 ASN
A 451 ASN
A 473 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.193630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.178333 restraints weight = 4278.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.176627 restraints weight = 7467.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.176703 restraints weight = 7316.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.175518 restraints weight = 7181.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.175774 restraints weight = 6849.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.1259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4412  Z= 0.157
  Angle     :  0.592   5.945   6000  Z= 0.302
  Chirality :  0.040   0.137    711
  Planarity :  0.004   0.040    733
  Dihedral  :  8.645  80.030    640
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 21.09 %
    Favored  : 75.22 %
  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:  1.91 (0.37), residues: 552
  helix:  2.74 (0.26), residues: 365
  sheet:  0.03 (0.79), residues: 49
  loop : -2.57 (0.50), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  19 
 TYR   0.013   0.001   TYR A 459 
 PHE   0.014   0.001   PHE A 361 
 TRP   0.009   0.001   TRP A 161 
 HIS   0.002   0.001   HIS A 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 4410)
  covalent geometry    : angle       0.59156 ( 5996)
  SS BOND              : bond        0.00307 (    2)
  SS BOND              : angle       0.81061 (    4)
  hydrogen bonds       : bond        0.03856 (  320)
  hydrogen bonds       : angle       4.89137 (  939)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 55
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A  248 HIS cc_start: 0.7079 (OUTLIER) cc_final: 0.6325 (m-70)
REVERT: B  108 SER cc_start: 0.8728 (m) cc_final: 0.8503 (m)
  outliers start: 17
  outliers final: 9
  residues processed: 68
  average time/residue: 0.0884
  time to fit residues: 7.4223
Evaluate side-chains
  55 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  236 PHE
Chi-restraints excluded: chain A residue  248 HIS
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue    6 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0980
   chunk 17 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0060
   chunk 10 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 47 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.3796

-------------------------------------------------------------------------------
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 = 0.3929 r_free = 0.3929 target = 0.181075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.151474 restraints weight = 4338.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.149180 restraints weight = 6725.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.149814 restraints weight = 6803.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.149557 restraints weight = 5329.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.149660 restraints weight = 5200.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4412  Z= 0.126
  Angle     :  0.527   6.790   6000  Z= 0.268
  Chirality :  0.038   0.137    711
  Planarity :  0.004   0.053    733
  Dihedral  :  7.785  66.356    638
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 20.65 %
    Favored  : 76.52 %
  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 (0.37), residues: 552
  helix:  2.79 (0.26), residues: 364
  sheet:  0.43 (0.80), residues: 47
  loop : -2.04 (0.53), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 111 
 TYR   0.011   0.001   TYR A 493 
 PHE   0.011   0.001   PHE A 361 
 TRP   0.008   0.001   TRP A 161 
 HIS   0.002   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 4410)
  covalent geometry    : angle       0.52662 ( 5996)
  SS BOND              : bond        0.00337 (    2)
  SS BOND              : angle       0.38281 (    4)
  hydrogen bonds       : bond        0.03478 (  320)
  hydrogen bonds       : angle       4.55859 (  939)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A  248 HIS cc_start: 0.6475 (OUTLIER) cc_final: 0.5875 (m-70)
REVERT: B  108 SER cc_start: 0.8596 (m) cc_final: 0.8340 (m)
  outliers start: 13
  outliers final: 7
  residues processed: 55
  average time/residue: 0.0512
  time to fit residues: 3.7396
Evaluate side-chains
  52 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  248 HIS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue    6 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0970
   chunk 29 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   chunk 36 optimal weight:    6.9990
   chunk 26 optimal weight:    0.8980
   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 = 0.3915 r_free = 0.3915 target = 0.179737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.152575 restraints weight = 4354.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.148428 restraints weight = 5762.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.148694 restraints weight = 5890.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.148829 restraints weight = 5220.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.148859 restraints weight = 4932.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4412  Z= 0.136
  Angle     :  0.522   6.823   6000  Z= 0.266
  Chirality :  0.038   0.139    711
  Planarity :  0.004   0.054    733
  Dihedral  :  7.413  59.452    638
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 20.65 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.15 (0.37), residues: 552
  helix:  2.76 (0.26), residues: 364
  sheet:  0.57 (0.81), residues: 47
  loop : -2.08 (0.52), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 111 
 TYR   0.010   0.001   TYR A 335 
 PHE   0.009   0.001   PHE A 361 
 TRP   0.007   0.001   TRP A 161 
 HIS   0.003   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4410)
  covalent geometry    : angle       0.52190 ( 5996)
  SS BOND              : bond        0.00121 (    2)
  SS BOND              : angle       0.40375 (    4)
  hydrogen bonds       : bond        0.03418 (  320)
  hydrogen bonds       : angle       4.46716 (  939)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.119 
Fit side-chains
REVERT: B  108 SER cc_start: 0.8623 (m) cc_final: 0.8351 (m)
  outliers start: 17
  outliers final: 11
  residues processed: 67
  average time/residue: 0.0467
  time to fit residues: 4.2286
Evaluate side-chains
  57 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  236 PHE
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  497 ARG
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue    6 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0980
   chunk 15 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 2 optimal weight:    0.1980
   chunk 35 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.3879 r_free = 0.3879 target = 0.176952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.149888 restraints weight = 4387.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.147115 restraints weight = 5796.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.147253 restraints weight = 6285.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.146926 restraints weight = 5947.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.146941 restraints weight = 5746.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4412  Z= 0.121
  Angle     :  0.520   9.791   6000  Z= 0.259
  Chirality :  0.037   0.137    711
  Planarity :  0.004   0.055    733
  Dihedral  :  7.130  53.406    638
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 21.52 %
    Favored  : 75.00 %
  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:  2.23 (0.37), residues: 552
  helix:  2.80 (0.26), residues: 363
  sheet:  0.80 (0.82), residues: 47
  loop : -2.02 (0.53), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 111 
 TYR   0.010   0.001   TYR A 243 
 PHE   0.011   0.001   PHE A 361 
 TRP   0.007   0.001   TRP A 161 
 HIS   0.005   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 4410)
  covalent geometry    : angle       0.51981 ( 5996)
  SS BOND              : bond        0.00144 (    2)
  SS BOND              : angle       0.37715 (    4)
  hydrogen bonds       : bond        0.03250 (  320)
  hydrogen bonds       : angle       4.34309 (  939)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A  248 HIS cc_start: 0.6636 (OUTLIER) cc_final: 0.6171 (m-70)
REVERT: B  108 SER cc_start: 0.8607 (m) cc_final: 0.8347 (m)
  outliers start: 16
  outliers final: 12
  residues processed: 69
  average time/residue: 0.0474
  time to fit residues: 4.5195
Evaluate side-chains
  62 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  236 PHE
Chi-restraints excluded: chain A residue  248 HIS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue    6 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 40 optimal weight:    9.9990
   chunk 3 optimal weight:    0.4980
   chunk 8 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.179397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.159268 restraints weight = 4442.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.148597 restraints weight = 9259.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.145135 restraints weight = 6861.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.145846 restraints weight = 7624.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.146449 restraints weight = 5681.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   4412  Z= 0.149
  Angle     :  0.543   7.984   6000  Z= 0.274
  Chirality :  0.038   0.138    711
  Planarity :  0.004   0.055    733
  Dihedral  :  7.118  55.340    638
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 23.04 %
    Favored  : 73.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.09 (0.37), residues: 552
  helix:  2.67 (0.26), residues: 362
  sheet:  0.76 (0.80), residues: 47
  loop : -2.00 (0.52), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 111 
 TYR   0.012   0.001   TYR A 335 
 PHE   0.012   0.001   PHE A 200 
 TRP   0.006   0.001   TRP A 161 
 HIS   0.005   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 4410)
  covalent geometry    : angle       0.54324 ( 5996)
  SS BOND              : bond        0.00149 (    2)
  SS BOND              : angle       0.44050 (    4)
  hydrogen bonds       : bond        0.03458 (  320)
  hydrogen bonds       : angle       4.41889 (  939)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  248 HIS cc_start: 0.6624 (OUTLIER) cc_final: 0.6232 (m-70)
REVERT: B  108 SER cc_start: 0.8675 (m) cc_final: 0.8430 (m)
  outliers start: 14
  outliers final: 11
  residues processed: 63
  average time/residue: 0.0510
  time to fit residues: 4.3142
Evaluate side-chains
  61 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  236 PHE
Chi-restraints excluded: chain A residue  248 HIS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue    6 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 8 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0570
   chunk 5 optimal weight:    0.4980
   chunk 35 optimal weight:    0.8980
   chunk 40 optimal weight:    9.9990
   chunk 52 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.5298

-------------------------------------------------------------------------------
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 = 0.3927 r_free = 0.3927 target = 0.180866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.153774 restraints weight = 4425.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.148020 restraints weight = 7828.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.148777 restraints weight = 7407.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.148756 restraints weight = 6272.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.149020 restraints weight = 5654.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4412  Z= 0.132
  Angle     :  0.526   7.816   6000  Z= 0.263
  Chirality :  0.038   0.135    711
  Planarity :  0.004   0.055    733
  Dihedral  :  6.872  57.875    636
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 23.04 %
    Favored  : 73.70 %
  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:  2.12 (0.37), residues: 552
  helix:  2.67 (0.26), residues: 362
  sheet:  0.86 (0.79), residues: 47
  loop : -1.96 (0.52), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 111 
 TYR   0.010   0.001   TYR A 335 
 PHE   0.009   0.001   PHE A 200 
 TRP   0.007   0.001   TRP A 161 
 HIS   0.003   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4410)
  covalent geometry    : angle       0.52573 ( 5996)
  SS BOND              : bond        0.00149 (    2)
  SS BOND              : angle       0.42785 (    4)
  hydrogen bonds       : bond        0.03254 (  320)
  hydrogen bonds       : angle       4.33386 (  939)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A  248 HIS cc_start: 0.6712 (OUTLIER) cc_final: 0.6369 (m-70)
REVERT: A  253 LEU cc_start: 0.4827 (OUTLIER) cc_final: 0.4558 (tp)
REVERT: B  108 SER cc_start: 0.8645 (m) cc_final: 0.8402 (m)
  outliers start: 15
  outliers final: 12
  residues processed: 65
  average time/residue: 0.0474
  time to fit residues: 4.1363
Evaluate side-chains
  65 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  236 PHE
Chi-restraints excluded: chain A residue  248 HIS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue    6 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0060
   chunk 12 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 40 optimal weight:   10.0000
   chunk 30 optimal weight:    0.0000
   chunk 54 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.4400

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

Flipped N/Q/H residues before XYZ refinement:
** B  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.177130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.149195 restraints weight = 4401.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.145250 restraints weight = 5849.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.145457 restraints weight = 6195.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.145410 restraints weight = 5568.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.145433 restraints weight = 5384.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4412  Z= 0.123
  Angle     :  0.520   7.949   6000  Z= 0.260
  Chirality :  0.038   0.137    711
  Planarity :  0.004   0.055    733
  Dihedral  :  6.729  58.769    636
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 23.04 %
    Favored  : 73.70 %
  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:  2.11 (0.37), residues: 552
  helix:  2.70 (0.26), residues: 364
  sheet:  0.15 (0.75), residues: 57
  loop : -1.96 (0.54), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 111 
 TYR   0.010   0.001   TYR A 335 
 PHE   0.010   0.001   PHE A 361 
 TRP   0.007   0.001   TRP A 161 
 HIS   0.003   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 4410)
  covalent geometry    : angle       0.51978 ( 5996)
  SS BOND              : bond        0.00138 (    2)
  SS BOND              : angle       0.45721 (    4)
  hydrogen bonds       : bond        0.03140 (  320)
  hydrogen bonds       : angle       4.28121 (  939)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 49
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  248 HIS cc_start: 0.6639 (OUTLIER) cc_final: 0.6252 (m-70)
REVERT: A  253 LEU cc_start: 0.5028 (OUTLIER) cc_final: 0.4770 (tp)
REVERT: A  410 MET cc_start: 0.8080 (tmm) cc_final: 0.7765 (tmm)
REVERT: B  108 SER cc_start: 0.8635 (m) cc_final: 0.8376 (m)
  outliers start: 15
  outliers final: 9
  residues processed: 63
  average time/residue: 0.0698
  time to fit residues: 5.6590
Evaluate side-chains
  58 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  236 PHE
Chi-restraints excluded: chain A residue  248 HIS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain B residue    5 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0020
   chunk 24 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 38 optimal weight:    0.2980
   chunk 6 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 16 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.4788

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

Flipped N/Q/H residues before XYZ refinement:
** B  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.177101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.141163 restraints weight = 4471.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.141204 restraints weight = 4297.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.141204 restraints weight = 4271.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.141204 restraints weight = 4271.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.141204 restraints weight = 4271.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.2449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4412  Z= 0.127
  Angle     :  0.529   7.974   6000  Z= 0.264
  Chirality :  0.038   0.139    711
  Planarity :  0.004   0.055    733
  Dihedral  :  6.037  50.077    633
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 23.26 %
    Favored  : 74.13 %
  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:  2.13 (0.37), residues: 552
  helix:  2.69 (0.26), residues: 363
  sheet:  0.37 (0.75), residues: 57
  loop : -1.99 (0.54), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 111 
 TYR   0.009   0.001   TYR A 459 
 PHE   0.009   0.001   PHE A 361 
 TRP   0.007   0.001   TRP A 161 
 HIS   0.003   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4410)
  covalent geometry    : angle       0.52894 ( 5996)
  SS BOND              : bond        0.00110 (    2)
  SS BOND              : angle       0.45440 (    4)
  hydrogen bonds       : bond        0.03151 (  320)
  hydrogen bonds       : angle       4.29138 (  939)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A  196 MET cc_start: 0.6360 (mmp) cc_final: 0.6128 (tpp)
REVERT: A  248 HIS cc_start: 0.6513 (OUTLIER) cc_final: 0.6117 (m-70)
REVERT: A  253 LEU cc_start: 0.4964 (OUTLIER) cc_final: 0.4721 (tp)
REVERT: B  108 SER cc_start: 0.8577 (m) cc_final: 0.8277 (m)
  outliers start: 12
  outliers final: 9
  residues processed: 58
  average time/residue: 0.0635
  time to fit residues: 4.9269
Evaluate side-chains
  57 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  236 PHE
Chi-restraints excluded: chain A residue  248 HIS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain B residue    5 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0570
   chunk 43 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 20 optimal weight:    7.9990
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
** B  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.175318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.144760 restraints weight = 4451.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.141149 restraints weight = 6050.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.141895 restraints weight = 6359.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.141783 restraints weight = 5830.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.141840 restraints weight = 5375.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4412  Z= 0.147
  Angle     :  0.548   7.698   6000  Z= 0.274
  Chirality :  0.038   0.141    711
  Planarity :  0.004   0.055    733
  Dihedral  :  5.757  46.608    633
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 23.04 %
    Favored  : 74.13 %
  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:  2.12 (0.37), residues: 552
  helix:  2.59 (0.26), residues: 361
  sheet:  1.35 (0.81), residues: 47
  loop : -1.87 (0.53), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 111 
 TYR   0.010   0.001   TYR A 459 
 PHE   0.009   0.001   PHE B  68 
 TRP   0.006   0.001   TRP A 161 
 HIS   0.002   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 4410)
  covalent geometry    : angle       0.54842 ( 5996)
  SS BOND              : bond        0.00113 (    2)
  SS BOND              : angle       0.42593 (    4)
  hydrogen bonds       : bond        0.03325 (  320)
  hydrogen bonds       : angle       4.36795 (  939)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.145 
Fit side-chains
REVERT: A  196 MET cc_start: 0.6630 (mmp) cc_final: 0.6428 (tpp)
REVERT: A  253 LEU cc_start: 0.5062 (OUTLIER) cc_final: 0.4821 (tp)
REVERT: B   77 ASN cc_start: 0.7374 (t0) cc_final: 0.7126 (t0)
REVERT: B  108 SER cc_start: 0.8607 (m) cc_final: 0.8322 (m)
  outliers start: 13
  outliers final: 10
  residues processed: 62
  average time/residue: 0.0613
  time to fit residues: 5.1020
Evaluate side-chains
  60 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  112 HIS
Chi-restraints excluded: chain A residue  236 PHE
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  298 CYS
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  443 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 48 optimal weight:    0.1980
   chunk 31 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0010
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 50 optimal weight:    0.1980
   overall best weight:    0.3786

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

Flipped N/Q/H residues before XYZ refinement:
** B  77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.182724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.148416 restraints weight = 4415.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.148460 restraints weight = 4265.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.148460 restraints weight = 4241.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.148460 restraints weight = 4241.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.148460 restraints weight = 4241.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4412  Z= 0.118
  Angle     :  0.531   7.978   6000  Z= 0.263
  Chirality :  0.037   0.142    711
  Planarity :  0.004   0.054    733
  Dihedral  :  5.415  45.226    633
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 24.13 %
    Favored  : 73.70 %
  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:  2.18 (0.37), residues: 552
  helix:  2.69 (0.26), residues: 361
  sheet:  0.56 (0.76), residues: 57
  loop : -1.81 (0.53), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 111 
 TYR   0.009   0.001   TYR A 459 
 PHE   0.017   0.001   PHE B  68 
 TRP   0.008   0.001   TRP A 161 
 HIS   0.003   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 4410)
  covalent geometry    : angle       0.53075 ( 5996)
  SS BOND              : bond        0.00082 (    2)
  SS BOND              : angle       0.35548 (    4)
  hydrogen bonds       : bond        0.03049 (  320)
  hydrogen bonds       : angle       4.27749 (  939)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 713.90 seconds
wall clock time: 13 minutes 0.30 seconds (780.30 seconds total)