Starting phenix.real_space_refine
on Tue Feb  3 14:31:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p16_13157/02_2026/7p16_13157.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p16_13157/02_2026/7p16_13157.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p16_13157/02_2026/7p16_13157.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p16_13157/02_2026/7p16_13157.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p16_13157/02_2026/7p16_13157.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p16_13157/02_2026/7p16_13157.cif"
  }
  resolution = 4.3
  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=   0.003 sd=   0.099
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      23      5.16       5
     C    2412      2.51       5
     N     561      2.21       5
     O     624      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3621
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2617
          Classifications: {'peptide': 318}
          Link IDs: {'PTRANS': 7, 'TRANS': 310}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 964
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 3, 'TRANS': 122}
    Chain: "A"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'PLC': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
  Time building chain proxies: 0.98, per 1000 atoms: 0.27
  Number of scatterers: 3621
  At special positions: 0
  Unit cell: (76.818, 102.858, 70.308, 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      23     16.00
     P       1     15.00
     O     624      8.00
     N     561      7.00
     C    2412      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  28 " - pdb=" SG  CYS B 102 " 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: 0.29
  Conformation dependent library (CDL) restraints added in 131.9 milliseconds
  

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  824

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 3 sheets defined
      68.0% alpha, 13.1% 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 4 through 13
      removed outlier: 3.587A  pdb=" N   PHE A   8 " --> pdb=" O   THR A   4 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   MET A  10 " --> pdb=" O   CYS A   6 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 36
      removed outlier: 4.482A  pdb=" N   THR A  20 " --> pdb=" O   ILE A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 67
      removed outlier: 3.565A  pdb=" N   PHE A  47 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   VAL A  48 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL A  55 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 86
    Processing helix  chain 'A' and resid 87 through 105
      removed outlier: 3.605A  pdb=" N   PHE A  94 " --> pdb=" O   THR A  90 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   VAL A  95 " --> pdb=" O   ARG A  91 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU A  96 " --> pdb=" O   TYR A  92 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   HIS A 101 " --> pdb=" O   ARG A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 141
      removed outlier: 3.521A  pdb=" N   LEU A 134 " --> pdb=" O   ASP A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 156
      removed outlier: 4.092A  pdb=" N   LEU A 149 " --> pdb=" O   PRO A 145 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLU A 156 " --> pdb=" O   TYR A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 190
      removed outlier: 3.723A  pdb=" N   LEU A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 197
    Processing helix  chain 'A' and resid 198 through 227
      removed outlier: 4.140A  pdb=" N   LYS A 202 " --> pdb=" O   GLY A 198 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU A 214 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   VAL A 226 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 250
      removed outlier: 3.576A  pdb=" N   VAL A 231 " --> pdb=" O   ASP A 227 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE A 247 " --> pdb=" O   PHE A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 274
      removed outlier: 3.761A  pdb=" N   VAL A 272 " --> pdb=" O   GLY A 268 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   PHE A 273 " --> pdb=" O   PHE A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 281
      removed outlier: 4.394A  pdb=" N   GLN A 281 " --> pdb=" O   ILE A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 308
      removed outlier: 3.513A  pdb=" N   VAL A 293 " --> pdb=" O   CYS A 289 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU A 296 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 343
      removed outlier: 3.992A  pdb=" N   ILE A 319 " --> pdb=" O   SER A 315 " (cutoff:3.500A)
      Proline residue:  A 320  - end of helix
      removed outlier: 3.754A  pdb=" N   VAL A 326 " --> pdb=" O   SER A 322 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU A 329 " --> pdb=" O   ILE A 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 71
      removed outlier: 3.518A  pdb=" N   LYS B  71 " --> pdb=" O   ASP B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 97
      removed outlier: 3.684A  pdb=" N   THR B  97 " --> pdb=" O   PRO B  94 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 9 through 13
    Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 18
      removed outlier: 3.588A  pdb=" N   VAL B  18 " --> pdb=" O   THR B 129 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   VAL B 128 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ALA B  98 " --> pdb=" O   VAL B 128 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   TYR B 101 " --> pdb=" O   PHE B  43 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ALA B  55 " --> pdb=" O   TRP B  42 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   ARG B  44 " --> pdb=" O   GLY B  53 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   GLY B  53 " --> pdb=" O   ARG B  44 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 18
      removed outlier: 3.588A  pdb=" N   VAL B  18 " --> pdb=" O   THR B 129 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   VAL B 128 " --> pdb=" O   ALA B  98 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ALA B  98 " --> pdb=" O   VAL B 128 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   TYR B 101 " --> pdb=" O   PHE B  43 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   ALA B 105 " --> pdb=" O   TYR B  38 " (cutoff:3.500A)

    236 hydrogen bonds defined for protein.
    678 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: 0.63

  Time building geometry restraints manager: 0.39 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 526
        1.31 -     1.44: 1140
        1.44 -     1.56: 2016
        1.56 -     1.69: 2
        1.69 -     1.81: 34
  Bond restraints: 3718
  Sorted by residual:
  bond pdb=" C'  PLC A 401 "
       pdb=" O2  PLC A 401 "
    ideal  model  delta    sigma   weight residual
    1.332  1.425 -0.093 2.00e-02 2.50e+03 2.17e+01
  bond pdb=" CB  PLC A 401 "
       pdb=" O3  PLC A 401 "
    ideal  model  delta    sigma   weight residual
    1.327  1.420 -0.093 2.00e-02 2.50e+03 2.15e+01
  bond pdb=" C'  PLC A 401 "
       pdb=" C1' PLC A 401 "
    ideal  model  delta    sigma   weight residual
    1.503  1.553 -0.050 2.00e-02 2.50e+03 6.23e+00
  bond pdb=" C4  PLC A 401 "
       pdb=" C5  PLC A 401 "
    ideal  model  delta    sigma   weight residual
    1.511  1.558 -0.047 2.00e-02 2.50e+03 5.62e+00
  bond pdb=" CB  PLC A 401 "
       pdb=" C1B PLC A 401 "
    ideal  model  delta    sigma   weight residual
    1.504  1.551 -0.047 2.00e-02 2.50e+03 5.48e+00
  ... (remaining 3713 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.21: 5010
        3.21 -     6.42: 34
        6.42 -     9.64: 5
        9.64 -    12.85: 2
       12.85 -    16.06: 1
  Bond angle restraints: 5052
  Sorted by residual:
  angle pdb=" O3P PLC A 401 "
        pdb=" P   PLC A 401 "
        pdb=" O4P PLC A 401 "
      ideal   model   delta    sigma   weight residual
      93.62  109.68  -16.06 3.00e+00 1.11e-01 2.87e+01
  angle pdb=" C5  PLC A 401 "
        pdb=" N   PLC A 401 "
        pdb=" C7  PLC A 401 "
      ideal   model   delta    sigma   weight residual
     106.97  119.04  -12.07 3.00e+00 1.11e-01 1.62e+01
  angle pdb=" N   LEU B 114 "
        pdb=" CA  LEU B 114 "
        pdb=" C   LEU B 114 "
      ideal   model   delta    sigma   weight residual
     114.56  109.89    4.67 1.27e+00 6.20e-01 1.35e+01
  angle pdb=" C   ILE A 278 "
        pdb=" N   LYS A 279 "
        pdb=" CA  LYS A 279 "
      ideal   model   delta    sigma   weight residual
     121.54  128.39   -6.85 1.91e+00 2.74e-01 1.29e+01
  angle pdb=" O1P PLC A 401 "
        pdb=" P   PLC A 401 "
        pdb=" O2P PLC A 401 "
      ideal   model   delta    sigma   weight residual
     119.61  109.03   10.58 3.00e+00 1.11e-01 1.24e+01
  ... (remaining 5047 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.46: 2023
       30.46 -    60.92: 89
       60.92 -    91.38: 10
       91.38 -   121.85: 0
      121.85 -   152.31: 2
  Dihedral angle restraints: 2124
    sinusoidal: 827
      harmonic: 1297
  Sorted by residual:
  dihedral pdb=" C2' PLC A 401 "
           pdb=" C'  PLC A 401 "
           pdb=" C1' PLC A 401 "
           pdb=" O2  PLC A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     169.53   17.22  152.31     1      3.00e+01 1.11e-03 2.01e+01
  dihedral pdb=" C2' PLC A 401 "
           pdb=" C'  PLC A 401 "
           pdb=" C1' PLC A 401 "
           pdb=" O'  PLC A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -11.03 -161.60  150.57     1      3.00e+01 1.11e-03 2.00e+01
  dihedral pdb=" CA  ILE A  16 "
           pdb=" C   ILE A  16 "
           pdb=" N   ILE A  17 "
           pdb=" CA  ILE A  17 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.23   19.77     0      5.00e+00 4.00e-02 1.56e+01
  ... (remaining 2121 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 385
       0.033 -    0.067: 148
       0.067 -    0.100: 30
       0.100 -    0.133: 8
       0.133 -    0.166: 1
  Chirality restraints: 572
  Sorted by residual:
  chirality pdb=" C2  PLC A 401 "
            pdb=" C1  PLC A 401 "
            pdb=" C3  PLC A 401 "
            pdb=" O2  PLC A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.31   -2.48    0.17 2.00e-01 2.50e+01 6.91e-01
  chirality pdb=" CG  LEU B  87 "
            pdb=" CB  LEU B  87 "
            pdb=" CD1 LEU B  87 "
            pdb=" CD2 LEU B  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.71    0.12 2.00e-01 2.50e+01 3.62e-01
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.28e-01
  ... (remaining 569 not shown)

  Planarity restraints: 604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 190 "    0.027 5.00e-02 4.00e+02   4.06e-02 2.64e+00
        pdb=" N   PRO A 191 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 191 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 191 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  73 "    0.130 9.50e-02 1.11e+02   5.86e-02 2.24e+00
        pdb=" NE  ARG B  73 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  73 "    0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  73 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  73 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 123 "    0.006 2.00e-02 2.50e+03   1.29e-02 1.65e+00
        pdb=" CD  GLU A 123 "   -0.022 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 123 "    0.008 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 123 "    0.008 2.00e-02 2.50e+03
  ... (remaining 601 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 100
        2.72 -     3.27: 3862
        3.27 -     3.81: 5788
        3.81 -     4.36: 6594
        4.36 -     4.90: 11142
  Nonbonded interactions: 27486
  Sorted by model distance:
  nonbonded pdb=" O   THR A 139 "
            pdb=" N   GLY A 143 "
     model   vdw
     2.178 3.120
  nonbonded pdb=" NZ  LYS A 209 "
            pdb=" OG1 THR A 274 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" OG  SER A 132 "
            pdb=" OD2 ASP A 181 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OE1 GLU B  12 "
            pdb=" N   GLY B 125 "
     model   vdw
     2.347 3.120
  nonbonded pdb=" O   CYS B  28 "
            pdb=" OG1 THR B  84 "
     model   vdw
     2.357 3.040
  ... (remaining 27481 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:             0.360
  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:          0.050
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.560
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
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      :  0.004   0.093   3719  Z= 0.205
  Angle     :  0.733  16.060   5054  Z= 0.340
  Chirality :  0.037   0.166    572
  Planarity :  0.004   0.059    604
  Dihedral  : 16.470 152.308   1297
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.40), residues: 436
  helix:  0.55 (0.32), residues: 249
  sheet:  0.04 (0.84), residues: 44
  loop : -1.00 (0.54), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 264 
 TYR   0.017   0.001   TYR A  92 
 PHE   0.016   0.001   PHE A 275 
 TRP   0.007   0.001   TRP A 177 
 HIS   0.001   0.000   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 3718)
  covalent geometry    : angle       0.73320 ( 5052)
  SS BOND              : bond        0.00141 (    1)
  SS BOND              : angle       0.38125 (    2)
  hydrogen bonds       : bond        0.27497 (  231)
  hydrogen bonds       : angle       8.01179 (  678)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A  146 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8783 (tm-30)
REVERT: A  279 LYS cc_start: 0.7233 (tttt) cc_final: 0.6998 (mttt)
REVERT: B   42 TRP cc_start: 0.8513 (m100) cc_final: 0.7949 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0649
  time to fit residues: 10.3539
Evaluate side-chains
  114 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0060
   overall best weight:    0.5396

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

Flipped N/Q/H residues before XYZ refinement:
A 183 GLN
A 277 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.166775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.137502 restraints weight = 5153.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.135243 restraints weight = 7417.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.136738 restraints weight = 7244.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.136645 restraints weight = 5583.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.136758 restraints weight = 5291.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.2005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3719  Z= 0.141
  Angle     :  0.585   6.633   5054  Z= 0.301
  Chirality :  0.040   0.136    572
  Planarity :  0.004   0.053    604
  Dihedral  : 10.713 108.552    524
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  5.67 %
    Favored  : 94.07 %
  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 are not related in a simple way.
  whole:  0.65 (0.40), residues: 436
  helix:  1.11 (0.30), residues: 262
  sheet:  0.55 (0.79), residues: 50
  loop : -0.98 (0.61), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 264 
 TYR   0.017   0.001   TYR A 208 
 PHE   0.022   0.001   PHE A 225 
 TRP   0.007   0.001   TRP A 177 
 HIS   0.001   0.000   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 3718)
  covalent geometry    : angle       0.58463 ( 5052)
  SS BOND              : bond        0.00128 (    1)
  SS BOND              : angle       0.21638 (    2)
  hydrogen bonds       : bond        0.04776 (  231)
  hydrogen bonds       : angle       4.59017 (  678)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 0.078 
Fit side-chains
REVERT: A  259 MET cc_start: 0.8123 (mmp) cc_final: 0.7720 (mmp)
REVERT: B   37 ILE cc_start: 0.9146 (mm) cc_final: 0.8649 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0403
  time to fit residues: 7.0379
Evaluate side-chains
  117 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 9 optimal weight:    6.9990
   chunk 33 optimal weight:    0.6980
   chunk 40 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   chunk 7 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 121 HIS
A 183 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.165223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.136413 restraints weight = 5187.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.133872 restraints weight = 8074.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.134980 restraints weight = 7938.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.135040 restraints weight = 6458.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.135132 restraints weight = 6211.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.2745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3719  Z= 0.158
  Angle     :  0.597   7.449   5054  Z= 0.302
  Chirality :  0.040   0.145    572
  Planarity :  0.004   0.049    604
  Dihedral  :  9.288  77.230    524
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  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 are not related in a simple way.
  whole:  0.62 (0.40), residues: 436
  helix:  1.23 (0.30), residues: 262
  sheet:  0.32 (0.76), residues: 48
  loop : -1.23 (0.59), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 264 
 TYR   0.019   0.002   TYR A  92 
 PHE   0.016   0.001   PHE A  47 
 TRP   0.008   0.001   TRP A 177 
 HIS   0.001   0.000   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3718)
  covalent geometry    : angle       0.59714 ( 5052)
  SS BOND              : bond        0.00160 (    1)
  SS BOND              : angle       0.05127 (    2)
  hydrogen bonds       : bond        0.04152 (  231)
  hydrogen bonds       : angle       4.35203 (  678)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: A  202 LYS cc_start: 0.8514 (mttt) cc_final: 0.8289 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0645
  time to fit residues: 10.8921
Evaluate side-chains
  119 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0370
   chunk 9 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
A 121 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.168329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.142843 restraints weight = 5076.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.141004 restraints weight = 7779.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.141541 restraints weight = 7216.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.140116 restraints weight = 6496.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.140603 restraints weight = 6269.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3719  Z= 0.135
  Angle     :  0.580   7.355   5054  Z= 0.292
  Chirality :  0.040   0.132    572
  Planarity :  0.004   0.055    604
  Dihedral  :  8.370  62.812    524
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  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 are not related in a simple way.
  whole:  0.65 (0.40), residues: 436
  helix:  1.26 (0.30), residues: 264
  sheet:  0.34 (0.75), residues: 48
  loop : -1.30 (0.60), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  51 
 TYR   0.017   0.001   TYR A  92 
 PHE   0.013   0.001   PHE A 225 
 TRP   0.009   0.001   TRP A 177 
 HIS   0.003   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3718)
  covalent geometry    : angle       0.58021 ( 5052)
  SS BOND              : bond        0.00081 (    1)
  SS BOND              : angle       0.25203 (    2)
  hydrogen bonds       : bond        0.03655 (  231)
  hydrogen bonds       : angle       4.04895 (  678)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A   91 ARG cc_start: 0.7167 (ttm110) cc_final: 0.6867 (ttm110)
REVERT: B   42 TRP cc_start: 0.8510 (m100) cc_final: 0.7758 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.0695
  time to fit residues: 12.2088
Evaluate side-chains
  120 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 6 optimal weight:   10.0000
   chunk 31 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   chunk 27 optimal weight:    0.5980
   chunk 38 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    0.0370
   chunk 11 optimal weight:    0.2980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
A 121 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.170235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.143242 restraints weight = 5321.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.141077 restraints weight = 8629.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.142304 restraints weight = 8350.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.142023 restraints weight = 5917.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.142392 restraints weight = 5776.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.3386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3719  Z= 0.130
  Angle     :  0.594   7.533   5054  Z= 0.292
  Chirality :  0.039   0.134    572
  Planarity :  0.004   0.055    604
  Dihedral  :  8.169  62.074    524
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  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 are not related in a simple way.
  whole:  0.80 (0.40), residues: 436
  helix:  1.42 (0.30), residues: 263
  sheet:  0.10 (0.72), residues: 50
  loop : -1.19 (0.61), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B  73 
 TYR   0.018   0.001   TYR A  92 
 PHE   0.012   0.001   PHE A 225 
 TRP   0.011   0.001   TRP A 177 
 HIS   0.001   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 3718)
  covalent geometry    : angle       0.59394 ( 5052)
  SS BOND              : bond        0.00288 (    1)
  SS BOND              : angle       0.34133 (    2)
  hydrogen bonds       : bond        0.03543 (  231)
  hydrogen bonds       : angle       3.94380 (  678)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.103 
Fit side-chains
REVERT: A  202 LYS cc_start: 0.8562 (mttt) cc_final: 0.8176 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0633
  time to fit residues: 10.7777
Evaluate side-chains
  118 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 42 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   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 121 HIS
A 183 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.164782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.139925 restraints weight = 5274.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.137329 restraints weight = 9402.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.138659 restraints weight = 9076.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.138083 restraints weight = 6317.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.138387 restraints weight = 6588.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.3604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3719  Z= 0.156
  Angle     :  0.619   7.389   5054  Z= 0.306
  Chirality :  0.040   0.141    572
  Planarity :  0.004   0.055    604
  Dihedral  :  8.210  64.032    524
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  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 are not related in a simple way.
  whole:  0.82 (0.41), residues: 436
  helix:  1.40 (0.30), residues: 264
  sheet:  0.16 (0.74), residues: 50
  loop : -1.14 (0.63), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 264 
 TYR   0.020   0.002   TYR A  92 
 PHE   0.011   0.001   PHE A 207 
 TRP   0.013   0.001   TRP A 177 
 HIS   0.003   0.001   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3718)
  covalent geometry    : angle       0.61926 ( 5052)
  SS BOND              : bond        0.00107 (    1)
  SS BOND              : angle       0.40442 (    2)
  hydrogen bonds       : bond        0.03549 (  231)
  hydrogen bonds       : angle       3.93478 (  678)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 ARG cc_start: 0.7308 (mtt90) cc_final: 0.7088 (mtt90)
REVERT: B   42 TRP cc_start: 0.8518 (m100) cc_final: 0.7857 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0602
  time to fit residues: 10.1379
Evaluate side-chains
  119 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0370
   chunk 37 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 8 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.7060

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

Flipped N/Q/H residues before XYZ refinement:
A 121 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.170017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.141481 restraints weight = 5457.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.139815 restraints weight = 9006.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.141013 restraints weight = 8425.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.141200 restraints weight = 6125.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.141348 restraints weight = 5678.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.3707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3719  Z= 0.142
  Angle     :  0.623   7.397   5054  Z= 0.306
  Chirality :  0.040   0.131    572
  Planarity :  0.004   0.058    604
  Dihedral  :  8.109  61.874    524
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.41), residues: 436
  helix:  1.22 (0.30), residues: 267
  sheet:  0.47 (0.89), residues: 39
  loop : -1.01 (0.60), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 264 
 TYR   0.020   0.002   TYR A  92 
 PHE   0.023   0.001   PHE A  47 
 TRP   0.017   0.001   TRP A  62 
 HIS   0.002   0.001   HIS A  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 3718)
  covalent geometry    : angle       0.62339 ( 5052)
  SS BOND              : bond        0.00059 (    1)
  SS BOND              : angle       0.35362 (    2)
  hydrogen bonds       : bond        0.03554 (  231)
  hydrogen bonds       : angle       3.96569 (  678)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A   95 VAL cc_start: 0.7681 (m) cc_final: 0.5502 (m)
REVERT: A  202 LYS cc_start: 0.8565 (mttt) cc_final: 0.8314 (mttt)
REVERT: A  260 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7178 (mm-30)
REVERT: A  264 ARG cc_start: 0.7480 (mtt90) cc_final: 0.7118 (mtt90)
REVERT: A  343 TYR cc_start: 0.7287 (m-80) cc_final: 0.7063 (m-80)
REVERT: B   26 LEU cc_start: 0.6959 (mp) cc_final: 0.6640 (mp)
REVERT: B   42 TRP cc_start: 0.8567 (m100) cc_final: 0.7827 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0689
  time to fit residues: 11.4941
Evaluate side-chains
  118 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 101 HIS
A 121 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.165650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.138430 restraints weight = 5200.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.136103 restraints weight = 9291.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.137253 restraints weight = 9124.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.137250 restraints weight = 6497.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.137428 restraints weight = 6240.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.3865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3719  Z= 0.148
  Angle     :  0.648   7.489   5054  Z= 0.320
  Chirality :  0.041   0.132    572
  Planarity :  0.004   0.059    604
  Dihedral  :  8.062  60.559    524
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.41), residues: 436
  helix:  1.22 (0.30), residues: 266
  sheet:  0.51 (0.90), residues: 39
  loop : -0.87 (0.61), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 264 
 TYR   0.033   0.001   TYR A  92 
 PHE   0.025   0.001   PHE A  47 
 TRP   0.013   0.001   TRP A 177 
 HIS   0.003   0.001   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 3718)
  covalent geometry    : angle       0.64838 ( 5052)
  SS BOND              : bond        0.00255 (    1)
  SS BOND              : angle       0.10659 (    2)
  hydrogen bonds       : bond        0.03471 (  231)
  hydrogen bonds       : angle       4.01504 (  678)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.128 
Fit side-chains
REVERT: B   42 TRP cc_start: 0.8572 (m100) cc_final: 0.7915 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0633
  time to fit residues: 10.0930
Evaluate side-chains
  117 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0870
   chunk 17 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 121 HIS
A 150 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.171355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.140708 restraints weight = 5225.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.140708 restraints weight = 5499.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.140707 restraints weight = 5499.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.140707 restraints weight = 5499.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.140707 restraints weight = 5499.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.4071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3719  Z= 0.139
  Angle     :  0.654   8.312   5054  Z= 0.323
  Chirality :  0.041   0.189    572
  Planarity :  0.004   0.061    604
  Dihedral  :  8.021  59.852    524
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.41), residues: 436
  helix:  1.19 (0.30), residues: 266
  sheet:  0.52 (0.87), residues: 39
  loop : -0.95 (0.60), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 264 
 TYR   0.036   0.002   TYR A  92 
 PHE   0.022   0.001   PHE A  47 
 TRP   0.032   0.002   TRP A  93 
 HIS   0.003   0.001   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 3718)
  covalent geometry    : angle       0.65435 ( 5052)
  SS BOND              : bond        0.00056 (    1)
  SS BOND              : angle       0.05227 (    2)
  hydrogen bonds       : bond        0.03561 (  231)
  hydrogen bonds       : angle       3.95993 (  678)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.078 
Fit side-chains
REVERT: A  248 ILE cc_start: 0.8584 (tp) cc_final: 0.8383 (tp)
REVERT: A  260 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7375 (mm-30)
REVERT: A  264 ARG cc_start: 0.7336 (mtt90) cc_final: 0.7090 (mtm-85)
REVERT: B   42 TRP cc_start: 0.8534 (m100) cc_final: 0.7895 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0489
  time to fit residues: 7.7291
Evaluate side-chains
  113 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0030
   chunk 17 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   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 121 HIS
** B  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.170177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.142907 restraints weight = 5288.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.140654 restraints weight = 7904.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.141836 restraints weight = 7550.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.141149 restraints weight = 5757.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.141398 restraints weight = 6185.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.4195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3719  Z= 0.136
  Angle     :  0.663   8.633   5054  Z= 0.327
  Chirality :  0.041   0.135    572
  Planarity :  0.004   0.059    604
  Dihedral  :  7.914  58.067    524
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.41), residues: 436
  helix:  1.31 (0.30), residues: 266
  sheet:  0.30 (0.73), residues: 50
  loop : -1.13 (0.64), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  51 
 TYR   0.029   0.001   TYR A  92 
 PHE   0.022   0.001   PHE A  47 
 TRP   0.019   0.002   TRP A  93 
 HIS   0.002   0.001   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3718)
  covalent geometry    : angle       0.66274 ( 5052)
  SS BOND              : bond        0.00190 (    1)
  SS BOND              : angle       0.20992 (    2)
  hydrogen bonds       : bond        0.03398 (  231)
  hydrogen bonds       : angle       3.88346 (  678)

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

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

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  872 Ramachandran restraints generated.
    436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.095 
Fit side-chains
REVERT: A  248 ILE cc_start: 0.8605 (tp) cc_final: 0.8379 (tp)
REVERT: A  260 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7359 (mm-30)
REVERT: A  264 ARG cc_start: 0.7340 (mtt90) cc_final: 0.7094 (mtm-85)
REVERT: B   42 TRP cc_start: 0.8542 (m100) cc_final: 0.7952 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0439
  time to fit residues: 7.0395
Evaluate side-chains
  111 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 16 optimal weight:   20.0000
   chunk 14 optimal weight:    0.9980
   chunk 37 optimal weight:    0.3980
   chunk 5 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 22 optimal weight:    7.9990
   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 101 HIS
A 121 HIS
A 183 GLN
** B  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.166181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.146587 restraints weight = 5139.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.138756 restraints weight = 7827.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.138157 restraints weight = 8028.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.136787 restraints weight = 9307.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.137265 restraints weight = 8524.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.4190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3719  Z= 0.150
  Angle     :  0.686   8.514   5054  Z= 0.337
  Chirality :  0.042   0.143    572
  Planarity :  0.004   0.059    604
  Dihedral  :  8.041  57.944    524
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.41), residues: 436
  helix:  1.19 (0.31), residues: 266
  sheet:  0.26 (0.75), residues: 50
  loop : -1.22 (0.63), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 264 
 TYR   0.030   0.002   TYR A  92 
 PHE   0.022   0.001   PHE A  47 
 TRP   0.028   0.002   TRP B 122 
 HIS   0.002   0.000   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 3718)
  covalent geometry    : angle       0.68655 ( 5052)
  SS BOND              : bond        0.00117 (    1)
  SS BOND              : angle       0.16579 (    2)
  hydrogen bonds       : bond        0.03533 (  231)
  hydrogen bonds       : angle       3.95981 (  678)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 675.69 seconds
wall clock time: 12 minutes 19.31 seconds (739.31 seconds total)