Starting phenix.real_space_refine
on Wed Sep 17 03:59:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xd0_38261/09_2025/8xd0_38261_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xd0_38261/09_2025/8xd0_38261.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xd0_38261/09_2025/8xd0_38261.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xd0_38261/09_2025/8xd0_38261.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xd0_38261/09_2025/8xd0_38261_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xd0_38261/09_2025/8xd0_38261_neut.cif"
  }
  resolution = 2.83
  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=   0.002
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       3      5.49       5
     S      14      5.16       5
     C    2124      2.51       5
     N     565      2.21       5
     O     651      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3357
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3285
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 417, 3267
          Classifications: {'peptide': 417}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 20, 'TRANS': 396}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
      Conformer: "B"
        Number of residues, atoms: 417, 3267
          Classifications: {'peptide': 417}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 20, 'TRANS': 396}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
          bond proxies already assigned to first conformer: 3319
    Chain: "A"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 72
          Unusual residues: {'AKG': 1, 'NDP': 1}
          Classifications: {'undetermined': 2, 'water': 14}
          Link IDs: {None: 15}
  Time building chain proxies: 1.92, per 1000 atoms: 0.57
  Number of scatterers: 3357
  At special positions: 0
  Unit cell: (66.176, 74.448, 72.192, 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      14     16.00
     P       3     15.00
     O     651      8.00
     N     565      7.00
     C    2124      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.25
  Conformation dependent library (CDL) restraints added in 273.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  766

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 2 sheets defined
      55.6% alpha, 13.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 19
    Processing helix  chain 'A' and resid 24 through 32
    Processing helix  chain 'A' and resid 79 through 97
      removed outlier: 3.519A  pdb=" N   TRP A  92 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   VAL A  97 " --> pdb=" O   LYS A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 115
    Processing helix  chain 'A' and resid 116 through 132
    Processing helix  chain 'A' and resid 133 through 135
      No H-bonds generated for 'chain 'A' and resid 133 through 135'
    Processing helix  chain 'A' and resid 149 through 165
    Processing helix  chain 'A' and resid 169 through 174
      removed outlier: 3.809A  pdb=" N   ILE A 174 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 207
    Processing helix  chain 'A' and resid 221 through 234
    Processing helix  chain 'A' and resid 256 through 268
    Processing helix  chain 'A' and resid 280 through 285
    Processing helix  chain 'A' and resid 302 through 307
      removed outlier: 4.707A  pdb=" N   ASP A 307 " --> pdb=" O   GLU A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 333
    Processing helix  chain 'A' and resid 339 through 344
    Processing helix  chain 'A' and resid 345 through 361
    Processing helix  chain 'A' and resid 365 through 392
    Processing helix  chain 'A' and resid 394 through 414
    Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45
      removed outlier: 4.617A  pdb=" N   THR A  55 " --> pdb=" O   ILE A 109 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   GLY A 103 " --> pdb=" O   HIS A  61 " (cutoff:3.500A)
      removed outlier: 5.268A  pdb=" N   LYS A  69 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
      removed outlier: 7.474A  pdb=" N   GLY A 106 " --> pdb=" O   LYS A  69 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   GLY A  71 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
      removed outlier: 7.963A  pdb=" N   ILE A 108 " --> pdb=" O   GLY A  71 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   ARG A  73 " --> pdb=" O   ILE A 108 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   THR A  68 " --> pdb=" O   ILE A 141 " (cutoff:3.500A)
      removed outlier: 8.071A  pdb=" N   ALA A 143 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   GLY A  70 " --> pdb=" O   ALA A 143 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279
      removed outlier: 3.617A  pdb=" N   VAL A 242 " --> pdb=" O   ILE A 249 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   ILE A 215 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL A 242 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   VAL A 217 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LYS A 214 " --> pdb=" O   VAL A 291 " (cutoff:3.500A)
      removed outlier: 8.340A  pdb=" N   ALA A 293 " --> pdb=" O   LYS A 214 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   ALA A 216 " --> pdb=" O   ALA A 293 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   LEU A 292 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   VAL A 314 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)

    180 hydrogen bonds defined for protein.
    517 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: 0.36 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1074
        1.34 -     1.45: 425
        1.45 -     1.57: 1893
        1.57 -     1.69: 3
        1.69 -     1.81: 27
  Bond restraints: 3422
  Sorted by residual:
  bond pdb=" O1N NDP A 500 "
       pdb=" PN  NDP A 500 "
    ideal  model  delta    sigma   weight residual
    1.477  1.548 -0.071 1.00e-02 1.00e+04 5.04e+01
  bond pdb=" O2B NDP A 500 "
       pdb=" P2B NDP A 500 "
    ideal  model  delta    sigma   weight residual
    1.833  1.569  0.264 3.80e-02 6.93e+02 4.84e+01
  bond pdb=" C   GLU A 114 "
       pdb=" CA BGLU A 114 "
    ideal  model  delta    sigma   weight residual
    1.523  1.611 -0.089 1.48e-02 4.57e+03 3.58e+01
  bond pdb=" O5D NDP A 500 "
       pdb=" PN  NDP A 500 "
    ideal  model  delta    sigma   weight residual
    1.757  1.559  0.198 3.50e-02 8.16e+02 3.20e+01
  bond pdb=" N   GLN A  19 "
       pdb=" CA BGLN A  19 "
    ideal  model  delta    sigma   weight residual
    1.459  1.528 -0.069 1.28e-02 6.10e+03 2.93e+01
  ... (remaining 3417 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.43: 4608
        4.43 -     8.86: 25
        8.86 -    13.29: 15
       13.29 -    17.72: 4
       17.72 -    22.15: 1
  Bond angle restraints: 4653
  Sorted by residual:
  angle pdb=" C1D NDP A 500 "
        pdb=" O4D NDP A 500 "
        pdb=" C4D NDP A 500 "
      ideal   model   delta    sigma   weight residual
     105.41  127.56  -22.15 2.71e+00 1.37e-01 6.70e+01
  angle pdb=" C5B NDP A 500 "
        pdb=" O5B NDP A 500 "
        pdb=" PA  NDP A 500 "
      ideal   model   delta    sigma   weight residual
     103.84  119.06  -15.22 1.91e+00 2.73e-01 6.32e+01
  angle pdb=" PA  NDP A 500 "
        pdb=" O3  NDP A 500 "
        pdb=" PN  NDP A 500 "
      ideal   model   delta    sigma   weight residual
     107.74  122.49  -14.75 1.95e+00 2.62e-01 5.70e+01
  angle pdb=" O1X NDP A 500 "
        pdb=" P2B NDP A 500 "
        pdb=" O3X NDP A 500 "
      ideal   model   delta    sigma   weight residual
     117.46  109.51    7.95 1.17e+00 7.36e-01 4.65e+01
  angle pdb=" N   ARG A  16 "
        pdb=" CA  ARG A  16 "
        pdb=" C   ARG A  16 "
      ideal   model   delta    sigma   weight residual
     112.23  104.47    7.76 1.26e+00 6.30e-01 3.79e+01
  ... (remaining 4648 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.47: 1872
       22.47 -    44.94: 122
       44.94 -    67.42: 29
       67.42 -    89.89: 10
       89.89 -   112.36: 1
  Dihedral angle restraints: 2034
    sinusoidal: 830
      harmonic: 1204
  Sorted by residual:
  dihedral pdb=" C5B NDP A 500 "
           pdb=" O5B NDP A 500 "
           pdb=" PA  NDP A 500 "
           pdb=" O3  NDP A 500 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.04   62.68  112.36     1      3.00e+01 1.11e-03 1.47e+01
  dihedral pdb=" C   GLU A  15 "
           pdb=" N   GLU A  15 "
           pdb=" CA BGLU A  15 "
           pdb=" CB BGLU A  15 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.06    8.46     0      2.50e+00 1.60e-01 1.15e+01
  dihedral pdb=" CB  GLU A 288 "
           pdb=" CG  GLU A 288 "
           pdb=" CD  GLU A 288 "
           pdb=" OE1 GLU A 288 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.69  -88.69     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 2031 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.144: 497
       0.144 -    0.289: 2
       0.289 -    0.433: 5
       0.433 -    0.577: 0
       0.577 -    0.721: 1
  Chirality restraints: 505
  Sorted by residual:
  chirality pdb=" C4B NDP A 500 "
            pdb=" C3B NDP A 500 "
            pdb=" C5B NDP A 500 "
            pdb=" O4B NDP A 500 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.87   -0.72 2.00e-01 2.50e+01 1.30e+01
  chirality pdb=" C4D NDP A 500 "
            pdb=" C3D NDP A 500 "
            pdb=" C5D NDP A 500 "
            pdb=" O4D NDP A 500 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.32   -0.40 2.00e-01 2.50e+01 3.92e+00
  chirality pdb=" C2D NDP A 500 "
            pdb=" C1D NDP A 500 "
            pdb=" C3D NDP A 500 "
            pdb=" O2D NDP A 500 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.34   -0.37 2.00e-01 2.50e+01 3.35e+00
  ... (remaining 502 not shown)

  Planarity restraints: 596
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C4N NDP A 500 "   -0.104 2.00e-02 2.50e+03   1.98e-01 3.91e+02
        pdb=" C5N NDP A 500 "    0.255 2.00e-02 2.50e+03
        pdb=" C6N NDP A 500 "   -0.262 2.00e-02 2.50e+03
        pdb=" N1N NDP A 500 "    0.110 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2N NDP A 500 "    0.059 2.00e-02 2.50e+03   1.00e-01 1.25e+02
        pdb=" C3N NDP A 500 "    0.166 2.00e-02 2.50e+03
        pdb=" C4N NDP A 500 "   -0.038 2.00e-02 2.50e+03
        pdb=" C7N NDP A 500 "   -0.106 2.00e-02 2.50e+03
        pdb=" N1N NDP A 500 "   -0.080 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 143 "   -0.044 5.00e-02 4.00e+02   6.79e-02 7.38e+00
        pdb=" N   PRO A 144 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 144 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 144 "   -0.037 5.00e-02 4.00e+02
  ... (remaining 593 not shown)

  Histogram of nonbonded interaction distances:
        2.45 -     2.94: 1404
        2.94 -     3.43: 3437
        3.43 -     3.92: 5864
        3.92 -     4.41: 6694
        4.41 -     4.90: 11033
  Nonbonded interactions: 28432
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 244 "
            pdb=" N   VAL A 270 "
     model   vdw
     2.449 3.120
  nonbonded pdb=" NZ  LYS A 229 "
            pdb=" OE2 GLU A 233 "
     model   vdw
     2.456 3.120
  nonbonded pdb=" O   VAL A 317 "
            pdb=" ND2 ASN A 344 "
     model   vdw
     2.469 3.120
  nonbonded pdb=" O   ILE A 174 "
            pdb=" NZ  LYS A 177 "
     model   vdw
     2.499 3.120
  nonbonded pdb=" OE1 GLU A 383 "
            pdb=" NH2 ARG A 406 "
     model   vdw
     2.511 3.120
  ... (remaining 28427 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=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.840
  Find NCS groups from input model:        0.020
  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:6.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
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      :  0.009   0.264   3422  Z= 0.379
  Angle     :  1.133  22.149   4653  Z= 0.583
  Chirality :  0.066   0.721    505
  Planarity :  0.010   0.198    596
  Dihedral  : 16.465 112.360   1268
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  :  3.23 %
    Favored  : 94.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.43), residues: 418
  helix:  1.92 (0.37), residues: 211
  sheet: -0.42 (0.67), residues: 66
  loop :  0.05 (0.55), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  65 
 TYR   0.007   0.001   TYR A 363 
 PHE   0.007   0.001   PHE A 341 
 TRP   0.009   0.001   TRP A  30 
 HIS   0.002   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00916 ( 3422)
  covalent geometry    : angle       1.13323 ( 4653)
  hydrogen bonds       : bond        0.13558 (  180)
  hydrogen bonds       : angle       5.83017 (  517)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.142 
Fit side-chains
  outliers start: 7
  outliers final: 3
  residues processed: 74
  average time/residue: 0.6514
  time to fit residues: 49.4270
Evaluate side-chains
  61 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  297 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 388 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.111189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.088650 restraints weight = 17367.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 3.57
r_work: 0.2705 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2668
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2668 r_free = 0.2668    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2668 r_free = 0.2668    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2668
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8806
moved from start:          0.1206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3422  Z= 0.132
  Angle     :  0.503   6.577   4653  Z= 0.262
  Chirality :  0.043   0.152    505
  Planarity :  0.005   0.057    596
  Dihedral  :  8.714 125.494    479
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 12.02 %
    Favored  : 84.75 %
  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:  1.72 (0.43), residues: 418
  helix:  2.26 (0.36), residues: 213
  sheet: -0.15 (0.68), residues: 68
  loop :  0.13 (0.58), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  16 
 TYR   0.009   0.001   TYR A 363 
 PHE   0.006   0.001   PHE A 381 
 TRP   0.008   0.001   TRP A 382 
 HIS   0.003   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 3422)
  covalent geometry    : angle       0.50347 ( 4653)
  hydrogen bonds       : bond        0.03801 (  180)
  hydrogen bonds       : angle       4.36095 (  517)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A    4 ILE cc_start: 0.8260 (mt) cc_final: 0.7948 (pp)
REVERT: A  218 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8658 (tm-30)
  outliers start: 10
  outliers final: 3
  residues processed: 67
  average time/residue: 0.5775
  time to fit residues: 39.8144
Evaluate side-chains
  62 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  297 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 28 optimal weight:    8.9990
   chunk 19 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 = 0.3175 r_free = 0.3175 target = 0.106355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.083746 restraints weight = 19450.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.2751 rms_B_bonded: 3.68
r_work: 0.2572 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.2572
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2489
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2489 r_free = 0.2489    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2489 r_free = 0.2489    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2489
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8846
moved from start:          0.1651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   3422  Z= 0.232
  Angle     :  0.571   8.660   4653  Z= 0.300
  Chirality :  0.046   0.129    505
  Planarity :  0.005   0.050    596
  Dihedral  :  8.527 131.180    479
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 14.96 %
    Favored  : 82.70 %
  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:  1.62 (0.43), residues: 418
  helix:  2.23 (0.35), residues: 212
  sheet: -0.12 (0.68), residues: 68
  loop : -0.03 (0.57), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 265 
 TYR   0.012   0.002   TYR A 363 
 PHE   0.011   0.002   PHE A   7 
 TRP   0.007   0.001   TRP A 382 
 HIS   0.010   0.002   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00573 ( 3422)
  covalent geometry    : angle       0.57139 ( 4653)
  hydrogen bonds       : bond        0.04756 (  180)
  hydrogen bonds       : angle       4.49410 (  517)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A   16 ARG cc_start: 0.8715 (ttt-90) cc_final: 0.8480 (ttt-90)
REVERT: A  218 GLN cc_start: 0.9219 (tm-30) cc_final: 0.8625 (tm-30)
REVERT: A  312 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8370 (mttt)
REVERT: A  351 SER cc_start: 0.9329 (t) cc_final: 0.9037 (m)
REVERT: A  389 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.7986 (mptt)
  outliers start: 7
  outliers final: 2
  residues processed: 70
  average time/residue: 0.5790
  time to fit residues: 41.6994
Evaluate side-chains
  67 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  312 LYS
Chi-restraints excluded: chain A residue  389 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 278 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 = 0.3240 r_free = 0.3240 target = 0.111311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.089805 restraints weight = 12564.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.2789 rms_B_bonded: 3.07
r_work: 0.2625 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2608
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2608 r_free = 0.2608    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2608 r_free = 0.2608    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2608
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8722
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   3422  Z= 0.106
  Angle     :  0.494   9.431   4653  Z= 0.255
  Chirality :  0.042   0.132    505
  Planarity :  0.005   0.047    596
  Dihedral  :  8.111 130.002    477
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 16.13 %
    Favored  : 82.40 %
  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:  1.76 (0.43), residues: 418
  helix:  2.41 (0.35), residues: 212
  sheet: -0.06 (0.68), residues: 68
  loop : -0.11 (0.58), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 265 
 TYR   0.007   0.001   TYR A 363 
 PHE   0.007   0.001   PHE A 341 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.008   0.002   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 3422)
  covalent geometry    : angle       0.49438 ( 4653)
  hydrogen bonds       : bond        0.03379 (  180)
  hydrogen bonds       : angle       4.20187 (  517)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.088 
Fit side-chains
REVERT: A   16 ARG cc_start: 0.8640 (ttt-90) cc_final: 0.8358 (ttt-90)
REVERT: A  218 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8436 (tm-30)
REVERT: A  389 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7950 (mptt)
  outliers start: 4
  outliers final: 1
  residues processed: 68
  average time/residue: 0.6617
  time to fit residues: 46.1052
Evaluate side-chains
  63 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 61
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 ASN
Chi-restraints excluded: chain A residue  389 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 39 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.107018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.085375 restraints weight = 11227.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.2755 rms_B_bonded: 2.89
r_work: 0.2598 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2622
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2622 r_free = 0.2622    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2622 r_free = 0.2622    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2622
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8806
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   3422  Z= 0.206
  Angle     :  0.556   9.752   4653  Z= 0.284
  Chirality :  0.045   0.127    505
  Planarity :  0.005   0.047    596
  Dihedral  :  8.162 133.466    475
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.65 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.30 %
    Favored  : 80.06 %
  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:  1.57 (0.43), residues: 418
  helix:  2.25 (0.35), residues: 212
  sheet: -0.13 (0.68), residues: 68
  loop : -0.18 (0.57), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 265 
 TYR   0.011   0.001   TYR A 363 
 PHE   0.010   0.002   PHE A 341 
 TRP   0.006   0.001   TRP A 382 
 HIS   0.007   0.002   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00510 ( 3422)
  covalent geometry    : angle       0.55590 ( 4653)
  hydrogen bonds       : bond        0.04435 (  180)
  hydrogen bonds       : angle       4.38902 (  517)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A    4 ILE cc_start: 0.7992 (mp) cc_final: 0.7513 (pp)
REVERT: A  218 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8511 (tm-30)
REVERT: A  312 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8278 (mttm)
REVERT: A  351 SER cc_start: 0.9280 (t) cc_final: 0.9002 (m)
REVERT: A  389 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7928 (mptt)
  outliers start: 8
  outliers final: 2
  residues processed: 69
  average time/residue: 0.6021
  time to fit residues: 42.7598
Evaluate side-chains
  62 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  312 LYS
Chi-restraints excluded: chain A residue  389 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0670
   chunk 7 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 37 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.9924

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

Flipped N/Q/H residues before XYZ refinement:
A 388 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.111454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.089965 restraints weight = 12253.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.2890 rms_B_bonded: 3.03
r_work: 0.2738 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2703
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2703 r_free = 0.2703    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2703 r_free = 0.2703    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2703
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8787
moved from start:          0.1753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3422  Z= 0.108
  Angle     :  0.493   8.532   4653  Z= 0.250
  Chirality :  0.043   0.138    505
  Planarity :  0.005   0.048    596
  Dihedral  :  7.870 133.200    473
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.65 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.89 %
    Favored  : 80.35 %
  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 (0.43), residues: 418
  helix:  2.40 (0.35), residues: 211
  sheet: -0.16 (0.67), residues: 68
  loop : -0.29 (0.57), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  16 
 TYR   0.007   0.001   TYR A 363 
 PHE   0.007   0.001   PHE A 341 
 TRP   0.007   0.001   TRP A 263 
 HIS   0.007   0.002   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 3422)
  covalent geometry    : angle       0.49331 ( 4653)
  hydrogen bonds       : bond        0.03408 (  180)
  hydrogen bonds       : angle       4.17850 (  517)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A  209 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8695 (m-30)
REVERT: A  218 GLN cc_start: 0.9055 (tm-30) cc_final: 0.8559 (tm-30)
  outliers start: 5
  outliers final: 2
  residues processed: 65
  average time/residue: 0.5865
  time to fit residues: 39.2162
Evaluate side-chains
  63 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  209 ASP
Chi-restraints excluded: chain A residue  270 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   chunk 27 optimal weight:    0.0980
   chunk 29 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 337 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.112784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.090745 restraints weight = 17580.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.2890 rms_B_bonded: 3.62
r_work: 0.2723 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2743
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2743 r_free = 0.2743    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2743 r_free = 0.2743    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2743
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8776
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3422  Z= 0.096
  Angle     :  0.476   7.524   4653  Z= 0.242
  Chirality :  0.042   0.129    505
  Planarity :  0.005   0.046    596
  Dihedral  :  7.741 132.607    473
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.65 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 19.65 %
    Favored  : 79.18 %
  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:  1.69 (0.43), residues: 418
  helix:  2.44 (0.35), residues: 211
  sheet: -0.03 (0.68), residues: 68
  loop : -0.30 (0.56), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  16 
 TYR   0.007   0.001   TYR A 408 
 PHE   0.007   0.001   PHE A 341 
 TRP   0.008   0.001   TRP A 263 
 HIS   0.007   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 3422)
  covalent geometry    : angle       0.47601 ( 4653)
  hydrogen bonds       : bond        0.03232 (  180)
  hydrogen bonds       : angle       4.07513 (  517)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A  218 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8537 (tm-30)
  outliers start: 3
  outliers final: 1
  residues processed: 64
  average time/residue: 0.5816
  time to fit residues: 38.3826
Evaluate side-chains
  59 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 27 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 9 optimal weight:    0.0070
   chunk 34 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 17 optimal weight:    5.9990
   overall best weight:    1.1602

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 388 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.111863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.090363 restraints weight = 12343.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 3.05
r_work: 0.2764 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2692
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2692 r_free = 0.2692    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2692 r_free = 0.2692    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2692
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8779
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3422  Z= 0.116
  Angle     :  0.490   7.948   4653  Z= 0.249
  Chirality :  0.043   0.127    505
  Planarity :  0.005   0.045    596
  Dihedral  :  7.787 133.524    473
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.65 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 19.94 %
    Favored  : 78.59 %
  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:  1.62 (0.43), residues: 418
  helix:  2.37 (0.35), residues: 211
  sheet: -0.06 (0.67), residues: 68
  loop : -0.33 (0.56), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  16 
 TYR   0.007   0.001   TYR A 363 
 PHE   0.008   0.001   PHE A 341 
 TRP   0.008   0.001   TRP A 263 
 HIS   0.007   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 3422)
  covalent geometry    : angle       0.48995 ( 4653)
  hydrogen bonds       : bond        0.03543 (  180)
  hydrogen bonds       : angle       4.09039 (  517)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A  218 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8652 (tm-30)
REVERT: A  312 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8234 (mttm)
  outliers start: 4
  outliers final: 1
  residues processed: 61
  average time/residue: 0.6574
  time to fit residues: 41.2168
Evaluate side-chains
  59 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  312 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 7 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 13 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0570
   overall best weight:    0.8500

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 GLN ** 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 = 0.3263 r_free = 0.3263 target = 0.113247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.090882 restraints weight = 18677.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.2874 rms_B_bonded: 3.72
r_work: 0.2701 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2675
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2675 r_free = 0.2675    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2675 r_free = 0.2675    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3422  Z= 0.103
  Angle     :  0.479   7.564   4653  Z= 0.244
  Chirality :  0.042   0.135    505
  Planarity :  0.005   0.047    596
  Dihedral  :  7.730 133.528    473
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.89 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 20.53 %
    Favored  : 78.30 %
  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:  1.62 (0.43), residues: 418
  helix:  2.40 (0.35), residues: 211
  sheet:  0.08 (0.71), residues: 63
  loop : -0.45 (0.55), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  16 
 TYR   0.007   0.001   TYR A 363 
 PHE   0.007   0.001   PHE A 341 
 TRP   0.008   0.001   TRP A 263 
 HIS   0.008   0.002   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 3422)
  covalent geometry    : angle       0.47868 ( 4653)
  hydrogen bonds       : bond        0.03347 (  180)
  hydrogen bonds       : angle       4.04334 (  517)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  218 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8684 (tm-30)
  outliers start: 3
  outliers final: 2
  residues processed: 55
  average time/residue: 0.6477
  time to fit residues: 36.6064
Evaluate side-chains
  55 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  280 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0980
   chunk 23 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 32 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 267 HIS ** 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 = 0.3254 r_free = 0.3254 target = 0.112528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.091187 restraints weight = 10342.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 2.85
r_work: 0.2771 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2779
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2779 r_free = 0.2779    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2779 r_free = 0.2779    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8751
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3422  Z= 0.119
  Angle     :  0.487   7.705   4653  Z= 0.249
  Chirality :  0.043   0.161    505
  Planarity :  0.005   0.046    596
  Dihedral  :  7.802 134.491    473
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.65 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 20.53 %
    Favored  : 78.30 %
  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:  1.57 (0.43), residues: 418
  helix:  2.37 (0.35), residues: 211
  sheet:  0.05 (0.71), residues: 63
  loop : -0.49 (0.55), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  16 
 TYR   0.008   0.001   TYR A 363 
 PHE   0.009   0.001   PHE A 341 
 TRP   0.008   0.001   TRP A 263 
 HIS   0.008   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 3422)
  covalent geometry    : angle       0.48665 ( 4653)
  hydrogen bonds       : bond        0.03546 (  180)
  hydrogen bonds       : angle       4.08271 (  517)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A  312 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8226 (mttt)
  outliers start: 3
  outliers final: 2
  residues processed: 56
  average time/residue: 0.5908
  time to fit residues: 34.0761
Evaluate side-chains
  59 residues out of total 337 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 VAL
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  312 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 218 GLN ** 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 = 0.3215 r_free = 0.3215 target = 0.109576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.087950 restraints weight = 11871.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 2.99
r_work: 0.2722 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2671
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2671 r_free = 0.2671    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2671 r_free = 0.2671    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2671
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8825
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3422  Z= 0.160
  Angle     :  0.514   7.628   4653  Z= 0.266
  Chirality :  0.044   0.177    505
  Planarity :  0.005   0.046    596
  Dihedral  :  8.091 139.099    473
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.41 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 20.53 %
    Favored  : 78.01 %
  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:  1.50 (0.43), residues: 418
  helix:  2.26 (0.35), residues: 212
  sheet: -0.00 (0.71), residues: 63
  loop : -0.44 (0.55), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  16 
 TYR   0.009   0.001   TYR A 363 
 PHE   0.011   0.001   PHE A 341 
 TRP   0.007   0.001   TRP A 382 
 HIS   0.007   0.002   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 3422)
  covalent geometry    : angle       0.51384 ( 4653)
  hydrogen bonds       : bond        0.04109 (  180)
  hydrogen bonds       : angle       4.23829 (  517)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1443.02 seconds
wall clock time: 25 minutes 19.92 seconds (1519.92 seconds total)