Starting phenix.real_space_refine
on Fri Aug 22 15:28:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bgu_16036/08_2025/8bgu_16036.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bgu_16036/08_2025/8bgu_16036.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bgu_16036/08_2025/8bgu_16036.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bgu_16036/08_2025/8bgu_16036.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bgu_16036/08_2025/8bgu_16036.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bgu_16036/08_2025/8bgu_16036.cif"
  }
  resolution = 4.1
  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=   0.005
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
     Zn      1      6.06       5
     P     121      5.49       5
     C    2457      2.51       5
     N     908      2.21       5
     O    1292      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4779
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "F"
      Number of atoms: 210
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 210
          Classifications: {'peptide': 42}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 36}
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 150
          Unresolved non-hydrogen angles: 195
          Unresolved non-hydrogen dihedrals: 136
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'TYR:plan': 1, 'TRP:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 90
    Chain: "3"
      Number of atoms: 2579
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2579
          Classifications: {'RNA': 121}
          Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 56, 'rna3p_pyr': 51}
          Link IDs: {'rna2p': 13, 'rna3p': 107}
    Chain: "A"
      Number of atoms: 1128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1128
          Classifications: {'peptide': 229}
          Incomplete info: {'truncation_to_alanine': 192}
          Link IDs: {'PTRANS': 9, 'TRANS': 219}
          Unresolved chain link angles: 9
          Unresolved non-hydrogen bonds: 745
          Unresolved non-hydrogen angles: 942
          Unresolved non-hydrogen dihedrals: 637
          Unresolved non-hydrogen chiralities: 50
          Planarities with less than four sites: {'TYR:plan': 17, 'ASN:plan1': 11, 'ARG:plan': 14, 'ASP:plan': 12, 'GLN:plan1': 6, 'GLU:plan': 17, 'HIS:plan': 5, 'PHE:plan': 6, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 420
    Chain: "B"
      Number of atoms: 861
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 861
          Classifications: {'peptide': 176}
          Incomplete info: {'truncation_to_alanine': 148}
          Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 169}
          Unresolved chain link angles: 5
          Unresolved non-hydrogen bonds: 573
          Unresolved non-hydrogen angles: 719
          Unresolved non-hydrogen dihedrals: 479
          Unresolved non-hydrogen chiralities: 44
          Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 8, 'GLU:plan': 14, 'ASN:plan1': 6, 'ARG:plan': 17, 'PHE:plan': 8, 'TYR:plan': 6, 'HIS:plan': 3, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 325
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.58, per 1000 atoms: 0.33
  Number of scatterers: 4779
  At special positions: 0
  Unit cell: (78.366, 102.723, 130.257, 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)
     Zn      1     29.99
     P     121     15.00
     O    1292      8.00
     N     908      7.00
     C    2457      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: 0.41
  Conformation dependent library (CDL) restraints added in 118.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  822

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 5 sheets defined
      35.1% alpha, 10.7% beta
      40 base pairs and 77 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'F' and resid 298 through 302
    Processing helix  chain 'A' and resid 81 through 86
      Proline residue:  A  84  - end of helix
      No H-bonds generated for 'chain 'A' and resid 81 through 86'
    Processing helix  chain 'A' and resid 94 through 114
    Processing helix  chain 'A' and resid 157 through 170
    Processing helix  chain 'A' and resid 192 through 200
    Processing helix  chain 'A' and resid 201 through 215
    Processing helix  chain 'A' and resid 216 through 223
    Processing helix  chain 'A' and resid 223 through 228
    Processing helix  chain 'A' and resid 235 through 250
    Processing helix  chain 'B' and resid 9 through 14
      removed outlier: 3.593A  pdb=" N   GLU B  14 " --> pdb=" O   ASN B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 45
    Processing helix  chain 'B' and resid 76 through 90
    Processing helix  chain 'B' and resid 138 through 144
      removed outlier: 3.525A  pdb=" N   ILE B 141 " --> pdb=" O   GLY B 138 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   ALA B 142 " --> pdb=" O   PHE B 139 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   LYS B 144 " --> pdb=" O   ILE B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 170
    Processing sheet with id=AA1, first strand: chain 'F' and resid 303 through 304
    Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 79
      removed outlier: 4.751A  pdb=" N   ASP A  72 " --> pdb=" O   ARG A  68 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   ARG A  68 " --> pdb=" O   ASP A  72 " (cutoff:3.500A)
      removed outlier: 5.412A  pdb=" N   ILE A  74 " --> pdb=" O   TYR A  66 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   TYR A  66 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 184
      removed outlier: 3.559A  pdb=" N   GLU A 189 " --> pdb=" O   ASP A 184 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 16 through 17
    Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 25

    128 hydrogen bonds defined for protein.
    360 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      99 hydrogen bonds
      166 hydrogen bond angles
      0 basepair planarities
      40 basepair parallelities
      77 stacking parallelities
  Total time for adding SS restraints: 0.68

  Time building geometry restraints manager: 0.57 seconds

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

  Histogram of bond lengths:
        1.22 -     1.30: 567
        1.30 -     1.38: 1132
        1.38 -     1.46: 1169
        1.46 -     1.54: 1922
        1.54 -     1.62: 289
  Bond restraints: 5079
  Sorted by residual:
  bond pdb=" C3'   G 3  52 "
       pdb=" O3'   G 3  52 "
    ideal  model  delta    sigma   weight residual
    1.417  1.442 -0.025 1.50e-02 4.44e+03 2.76e+00
  bond pdb=" CA  GLY A  87 "
       pdb=" C   GLY A  87 "
    ideal  model  delta    sigma   weight residual
    1.530  1.515  0.016 1.04e-02 9.25e+03 2.35e+00
  bond pdb=" C3'   C 3  98 "
       pdb=" O3'   C 3  98 "
    ideal  model  delta    sigma   weight residual
    1.417  1.439 -0.022 1.50e-02 4.44e+03 2.21e+00
  bond pdb=" N   GLY A  87 "
       pdb=" CA  GLY A  87 "
    ideal  model  delta    sigma   weight residual
    1.464  1.449  0.015 1.12e-02 7.97e+03 1.77e+00
  bond pdb=" N1    C 3  18 "
       pdb=" C2    C 3  18 "
    ideal  model  delta    sigma   weight residual
    1.397  1.420 -0.023 2.00e-02 2.50e+03 1.37e+00
  ... (remaining 5074 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 7188
        1.65 -     3.31: 272
        3.31 -     4.96: 54
        4.96 -     6.62: 18
        6.62 -     8.27: 7
  Bond angle restraints: 7539
  Sorted by residual:
  angle pdb=" C   GLU B   9 "
        pdb=" N   ASN B  10 "
        pdb=" CA  ASN B  10 "
      ideal   model   delta    sigma   weight residual
     120.06  127.14   -7.08 1.19e+00 7.06e-01 3.54e+01
  angle pdb=" O3'   C 3  98 "
        pdb=" C3'   C 3  98 "
        pdb=" C2'   C 3  98 "
      ideal   model   delta    sigma   weight residual
     113.70  121.40   -7.70 1.50e+00 4.44e-01 2.63e+01
  angle pdb=" O3'   G 3  52 "
        pdb=" C3'   G 3  52 "
        pdb=" C2'   G 3  52 "
      ideal   model   delta    sigma   weight residual
     113.70  120.98   -7.28 1.50e+00 4.44e-01 2.36e+01
  angle pdb=" C3'   G 3  52 "
        pdb=" O3'   G 3  52 "
        pdb=" P     U 3  53 "
      ideal   model   delta    sigma   weight residual
     120.20  126.68   -6.48 1.50e+00 4.44e-01 1.87e+01
  angle pdb=" N   GLY A  87 "
        pdb=" CA  GLY A  87 "
        pdb=" C   GLY A  87 "
      ideal   model   delta    sigma   weight residual
     111.67  115.60   -3.93 9.20e-01 1.18e+00 1.83e+01
  ... (remaining 7534 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.82: 2797
       32.82 -    65.64: 300
       65.64 -    98.46: 45
       98.46 -   131.28: 2
      131.28 -   164.10: 1
  Dihedral angle restraints: 3145
    sinusoidal: 1879
      harmonic: 1266
  Sorted by residual:
  dihedral pdb=" O4'   U 3 121 "
           pdb=" C1'   U 3 121 "
           pdb=" N1    U 3 121 "
           pdb=" C2    U 3 121 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   36.10 -164.10     1      1.70e+01 3.46e-03 6.52e+01
  dihedral pdb=" CA  LEU B  94 "
           pdb=" C   LEU B  94 "
           pdb=" N   ARG B  95 "
           pdb=" CA  ARG B  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.30  -24.70     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" C4'   C 3  98 "
           pdb=" C3'   C 3  98 "
           pdb=" O3'   C 3  98 "
           pdb=" P     G 3  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   98.39  121.61     1      3.50e+01 8.16e-04 1.19e+01
  ... (remaining 3142 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 926
       0.069 -    0.138: 87
       0.138 -    0.207: 1
       0.207 -    0.276: 0
       0.276 -    0.345: 2
  Chirality restraints: 1016
  Sorted by residual:
  chirality pdb=" C3'   C 3  98 "
            pdb=" C4'   C 3  98 "
            pdb=" O3'   C 3  98 "
            pdb=" C2'   C 3  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.13   -0.34 2.00e-01 2.50e+01 2.97e+00
  chirality pdb=" C3'   G 3  52 "
            pdb=" C4'   G 3  52 "
            pdb=" O3'   G 3  52 "
            pdb=" C2'   G 3  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.16   -0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" C1'   G 3   5 "
            pdb=" O4'   G 3   5 "
            pdb=" C2'   G 3   5 "
            pdb=" N9    G 3   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.32    0.14 2.00e-01 2.50e+01 4.93e-01
  ... (remaining 1013 not shown)

  Planarity restraints: 565
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A 3  92 "   -0.024 2.00e-02 2.50e+03   1.11e-02 3.40e+00
        pdb=" N9    A 3  92 "    0.027 2.00e-02 2.50e+03
        pdb=" C8    A 3  92 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    A 3  92 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    A 3  92 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A 3  92 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6    A 3  92 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A 3  92 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A 3  92 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    A 3  92 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    A 3  92 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G 3  67 "    0.024 2.00e-02 2.50e+03   1.01e-02 3.05e+00
        pdb=" N9    G 3  67 "   -0.018 2.00e-02 2.50e+03
        pdb=" C8    G 3  67 "   -0.008 2.00e-02 2.50e+03
        pdb=" N7    G 3  67 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    G 3  67 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    G 3  67 "    0.005 2.00e-02 2.50e+03
        pdb=" O6    G 3  67 "    0.011 2.00e-02 2.50e+03
        pdb=" N1    G 3  67 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    G 3  67 "   -0.009 2.00e-02 2.50e+03
        pdb=" N2    G 3  67 "   -0.000 2.00e-02 2.50e+03
        pdb=" N3    G 3  67 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    G 3  67 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 191 "    0.008 2.00e-02 2.50e+03   1.66e-02 2.75e+00
        pdb=" C   ASN A 191 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ASN A 191 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ALA A 192 "    0.010 2.00e-02 2.50e+03
  ... (remaining 562 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 909
        2.77 -     3.30: 3973
        3.30 -     3.83: 9635
        3.83 -     4.37: 9745
        4.37 -     4.90: 13364
  Nonbonded interactions: 37626
  Sorted by model distance:
  nonbonded pdb=" O6    G 3   1 "
            pdb=" O4    U 3 121 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O2'   G 3  77 "
            pdb=" O6    G 3 101 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" O6    G 3  67 "
            pdb=" O4    U 3 111 "
     model   vdw
     2.329 2.432
  nonbonded pdb=" O2    U 3  81 "
            pdb=" N2    G 3  99 "
     model   vdw
     2.333 2.496
  nonbonded pdb=" O4    U 3  81 "
            pdb=" O6    G 3  99 "
     model   vdw
     2.379 2.432
  ... (remaining 37621 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:             0.540
  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:                    0.020
  Process input model:                     7.760
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
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      :  0.003   0.025   5079  Z= 0.188
  Angle     :  0.839   8.272   7539  Z= 0.452
  Chirality :  0.041   0.345   1016
  Planarity :  0.003   0.017    565
  Dihedral  : 23.471 164.097   2323
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.24 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.58 (0.34), residues: 441
  helix: -1.54 (0.31), residues: 142
  sheet: -0.77 (0.74), residues: 55
  loop : -2.07 (0.36), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR F 302 
 PHE   0.000   0.000   PHE A 113 
 TRP   0.000   0.000   TRP F 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 5079)
  covalent geometry    : angle       0.83860 ( 7539)
  hydrogen bonds       : bond        0.12779 (  227)
  hydrogen bonds       : angle       5.46473 (  526)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.118 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0246
  time to fit residues: 0.7161
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 48 optimal weight:   50.0000
   chunk 26 optimal weight:   30.0000
   chunk 2 optimal weight:   20.0000
   chunk 16 optimal weight:   30.0000
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:   20.0000
   chunk 50 optimal weight:   20.0000
   chunk 53 optimal weight:   10.0000
   overall best weight:    9.9996

-------------------------------------------------------------------------------
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 = 0.3020 r_free = 0.3020 target = 0.043443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.030666 restraints weight = 57891.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.031470 restraints weight = 33454.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.031988 restraints weight = 23538.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.032369 restraints weight = 18756.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.032628 restraints weight = 15992.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.2643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.2787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.036   5079  Z= 0.460
  Angle     :  0.857   6.156   7539  Z= 0.453
  Chirality :  0.046   0.250   1016
  Planarity :  0.004   0.015    565
  Dihedral  : 24.490 163.139   2323
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 29.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.24 %
    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: -1.77 (0.38), residues: 441
  helix: -0.01 (0.41), residues: 143
  sheet: -1.30 (0.68), residues: 54
  loop : -1.91 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR F 302 
 PHE   0.000   0.000   PHE A 113 
 TRP   0.000   0.000   TRP F 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00776 ( 5079)
  covalent geometry    : angle       0.85745 ( 7539)
  hydrogen bonds       : bond        0.10926 (  227)
  hydrogen bonds       : angle       5.12575 (  526)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.110 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0238
  time to fit residues: 0.7253
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 3 optimal weight:   30.0000
   chunk 20 optimal weight:   10.0000
   chunk 19 optimal weight:    0.5980
   chunk 42 optimal weight:    8.9990
   chunk 12 optimal weight:   20.0000
   chunk 49 optimal weight:   10.0000
   chunk 4 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   chunk 14 optimal weight:   10.0000
   overall best weight:    4.6986

-------------------------------------------------------------------------------
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 = 0.3063 r_free = 0.3063 target = 0.044712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.031675 restraints weight = 55582.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.032539 restraints weight = 32031.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.033085 restraints weight = 22286.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.033503 restraints weight = 17640.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.033736 restraints weight = 14961.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.018   5079  Z= 0.228
  Angle     :  0.584   5.202   7539  Z= 0.312
  Chirality :  0.037   0.224   1016
  Planarity :  0.003   0.009    565
  Dihedral  : 24.022 164.353   2323
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 19.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.24 %
    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: -1.16 (0.40), residues: 441
  helix:  0.98 (0.45), residues: 143
  sheet: -1.57 (0.84), residues: 37
  loop : -1.74 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR F 302 
 PHE   0.000   0.000   PHE A 113 
 TRP   0.000   0.000   TRP F 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 5079)
  covalent geometry    : angle       0.58428 ( 7539)
  hydrogen bonds       : bond        0.06600 (  227)
  hydrogen bonds       : angle       4.35054 (  526)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.113 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0234
  time to fit residues: 0.7025
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 53 optimal weight:   20.0000
   chunk 20 optimal weight:    9.9990
   chunk 12 optimal weight:   20.0000
   chunk 33 optimal weight:   20.0000
   chunk 19 optimal weight:    6.9990
   chunk 42 optimal weight:   20.0000
   chunk 45 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 3 optimal weight:   30.0000
   overall best weight:    6.1990

-------------------------------------------------------------------------------
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 = 0.3006 r_free = 0.3006 target = 0.043102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2590 r_free = 0.2590 target = 0.030619 restraints weight = 57675.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.031435 restraints weight = 33375.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.031977 restraints weight = 23234.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.032317 restraints weight = 18397.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.032562 restraints weight = 15778.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.2643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.3746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.026   5079  Z= 0.307
  Angle     :  0.682   5.602   7539  Z= 0.361
  Chirality :  0.041   0.244   1016
  Planarity :  0.003   0.010    565
  Dihedral  : 24.276 159.732   2323
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 26.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.56 %
    Favored  : 88.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.24 %
    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: -1.38 (0.39), residues: 441
  helix:  0.87 (0.44), residues: 143
  sheet: -1.39 (0.79), residues: 42
  loop : -1.99 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR F 302 
 PHE   0.000   0.000   PHE A 113 
 TRP   0.000   0.000   TRP F 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 ( 5079)
  covalent geometry    : angle       0.68161 ( 7539)
  hydrogen bonds       : bond        0.08544 (  227)
  hydrogen bonds       : angle       4.69324 (  526)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.112 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0241
  time to fit residues: 0.7328
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 16 optimal weight:   30.0000
   chunk 41 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 44 optimal weight:   30.0000
   chunk 20 optimal weight:    7.9990
   chunk 50 optimal weight:   30.0000
   chunk 47 optimal weight:   20.0000
   chunk 5 optimal weight:   10.0000
   chunk 34 optimal weight:   20.0000
   chunk 1 optimal weight:   30.0000
   overall best weight:    8.5992

-------------------------------------------------------------------------------
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 = 0.2969 r_free = 0.2969 target = 0.041676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2555 r_free = 0.2555 target = 0.029557 restraints weight = 59071.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.030305 restraints weight = 34122.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2605 r_free = 0.2605 target = 0.030805 restraints weight = 24059.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.2619 r_free = 0.2619 target = 0.031161 restraints weight = 18997.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.031334 restraints weight = 16172.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.4727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.029   5079  Z= 0.417
  Angle     :  0.796   6.917   7539  Z= 0.423
  Chirality :  0.044   0.237   1016
  Planarity :  0.004   0.013    565
  Dihedral  : 24.625 159.323   2323
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 32.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.24 %
    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: -1.96 (0.38), residues: 441
  helix:  0.10 (0.43), residues: 135
  sheet: -1.34 (0.99), residues: 28
  loop : -2.14 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR F 302 
 PHE   0.000   0.000   PHE A 113 
 TRP   0.000   0.000   TRP F 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00704 ( 5079)
  covalent geometry    : angle       0.79619 ( 7539)
  hydrogen bonds       : bond        0.09896 (  227)
  hydrogen bonds       : angle       5.39724 (  526)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.110 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0240
  time to fit residues: 0.7089
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 29 optimal weight:   30.0000
   chunk 54 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0970
   chunk 10 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 16 optimal weight:   30.0000
   chunk 31 optimal weight:    3.9990
   overall best weight:    2.9984

-------------------------------------------------------------------------------
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 = 0.3045 r_free = 0.3045 target = 0.043989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.031291 restraints weight = 56812.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.032098 restraints weight = 32351.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.032684 restraints weight = 22676.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.033074 restraints weight = 17651.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.033241 restraints weight = 14876.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.4098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   5079  Z= 0.166
  Angle     :  0.535   5.090   7539  Z= 0.285
  Chirality :  0.035   0.221   1016
  Planarity :  0.002   0.008    565
  Dihedral  : 23.735 161.531   2323
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 14.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.24 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.41), residues: 441
  helix:  1.36 (0.45), residues: 142
  sheet: -1.35 (1.02), residues: 28
  loop : -1.73 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR F 302 
 PHE   0.000   0.000   PHE A 113 
 TRP   0.000   0.000   TRP F 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 5079)
  covalent geometry    : angle       0.53457 ( 7539)
  hydrogen bonds       : bond        0.05950 (  227)
  hydrogen bonds       : angle       4.20177 (  526)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.066 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0240
  time to fit residues: 0.6981
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 14 optimal weight:   10.0000
   chunk 16 optimal weight:   40.0000
   chunk 40 optimal weight:   20.0000
   chunk 51 optimal weight:    7.9990
   chunk 17 optimal weight:   10.0000
   chunk 47 optimal weight:   20.0000
   chunk 37 optimal weight:   20.0000
   chunk 18 optimal weight:   10.0000
   chunk 12 optimal weight:   20.0000
   chunk 1 optimal weight:   30.0000
   overall best weight:    8.7996

-------------------------------------------------------------------------------
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 = 0.2970 r_free = 0.2970 target = 0.041568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2548 r_free = 0.2548 target = 0.029528 restraints weight = 59377.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2579 r_free = 0.2579 target = 0.030284 restraints weight = 33975.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2597 r_free = 0.2597 target = 0.030767 restraints weight = 23766.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.031103 restraints weight = 18864.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2619 r_free = 0.2619 target = 0.031342 restraints weight = 16064.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8654
moved from start:          0.4854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.031   5079  Z= 0.414
  Angle     :  0.773   6.560   7539  Z= 0.410
  Chirality :  0.044   0.246   1016
  Planarity :  0.004   0.012    565
  Dihedral  : 24.386 158.639   2323
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 33.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.93 %
    Favored  : 87.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.24 %
    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: -1.79 (0.39), residues: 441
  helix:  0.19 (0.42), residues: 143
  sheet: -1.56 (0.80), residues: 40
  loop : -2.03 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR F 302 
 PHE   0.000   0.000   PHE A 113 
 TRP   0.000   0.000   TRP F 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00700 ( 5079)
  covalent geometry    : angle       0.77259 ( 7539)
  hydrogen bonds       : bond        0.09844 (  227)
  hydrogen bonds       : angle       5.18737 (  526)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.111 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0239
  time to fit residues: 0.7252
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 23 optimal weight:    0.0980
   chunk 32 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 4 optimal weight:    7.9990
   chunk 48 optimal weight:   40.0000
   chunk 40 optimal weight:   20.0000
   chunk 27 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 36 optimal weight:    8.9990
   chunk 13 optimal weight:   20.0000
   overall best weight:    5.4188

-------------------------------------------------------------------------------
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 = 0.3005 r_free = 0.3005 target = 0.042607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2582 r_free = 0.2582 target = 0.030231 restraints weight = 57791.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2613 r_free = 0.2613 target = 0.031017 restraints weight = 32920.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.031556 restraints weight = 23015.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.031925 restraints weight = 17998.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.032088 restraints weight = 15248.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.4672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.019   5079  Z= 0.267
  Angle     :  0.620   5.356   7539  Z= 0.330
  Chirality :  0.038   0.229   1016
  Planarity :  0.003   0.009    565
  Dihedral  : 24.039 160.172   2323
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 23.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.11 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.24 %
    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: -1.33 (0.40), residues: 441
  helix:  0.81 (0.44), residues: 143
  sheet: -1.61 (1.01), residues: 28
  loop : -1.85 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR F 302 
 PHE   0.000   0.000   PHE A 113 
 TRP   0.000   0.000   TRP F 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 5079)
  covalent geometry    : angle       0.61968 ( 7539)
  hydrogen bonds       : bond        0.07421 (  227)
  hydrogen bonds       : angle       4.61401 (  526)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.126 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0240
  time to fit residues: 0.7318
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 51 optimal weight:   20.0000
   chunk 1 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 13 optimal weight:   20.0000
   chunk 21 optimal weight:    3.9990
   chunk 33 optimal weight:   20.0000
   chunk 4 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   overall best weight:    7.1992

-------------------------------------------------------------------------------
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 = 0.2981 r_free = 0.2981 target = 0.041899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2561 r_free = 0.2561 target = 0.029768 restraints weight = 58069.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.030535 restraints weight = 32921.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2611 r_free = 0.2611 target = 0.031036 restraints weight = 23019.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.031391 restraints weight = 18073.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.031614 restraints weight = 15396.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.5102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.024   5079  Z= 0.338
  Angle     :  0.703   5.923   7539  Z= 0.373
  Chirality :  0.041   0.237   1016
  Planarity :  0.003   0.011    565
  Dihedral  : 24.284 158.445   2323
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 29.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.15 %
    Favored  : 86.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.24 %
    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 (0.39), residues: 441
  helix:  0.48 (0.43), residues: 142
  sheet: -1.69 (0.99), residues: 28
  loop : -1.98 (0.37), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR F 302 
 PHE   0.000   0.000   PHE A 113 
 TRP   0.000   0.000   TRP F 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00571 ( 5079)
  covalent geometry    : angle       0.70271 ( 7539)
  hydrogen bonds       : bond        0.08828 (  227)
  hydrogen bonds       : angle       4.99593 (  526)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.115 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0203
  time to fit residues: 0.6430
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 7 optimal weight:   10.0000
   chunk 3 optimal weight:   20.0000
   chunk 26 optimal weight:   30.0000
   chunk 45 optimal weight:   30.0000
   chunk 54 optimal weight:    1.9990
   chunk 50 optimal weight:   40.0000
   chunk 14 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   overall best weight:    6.5592

-------------------------------------------------------------------------------
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 = 0.2986 r_free = 0.2986 target = 0.041982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2566 r_free = 0.2566 target = 0.029869 restraints weight = 57568.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2597 r_free = 0.2597 target = 0.030661 restraints weight = 32856.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.031170 restraints weight = 22790.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.031523 restraints weight = 17906.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.031760 restraints weight = 15169.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.5153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.023   5079  Z= 0.311
  Angle     :  0.665   5.777   7539  Z= 0.354
  Chirality :  0.040   0.232   1016
  Planarity :  0.003   0.010    565
  Dihedral  : 24.149 158.602   2323
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 26.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.24 %
    Favored  : 87.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.24 %
    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: -1.48 (0.40), residues: 441
  helix:  0.64 (0.44), residues: 143
  sheet: -1.75 (0.99), residues: 28
  loop : -1.91 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR F 302 
 PHE   0.000   0.000   PHE A 113 
 TRP   0.000   0.000   TRP F 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 ( 5079)
  covalent geometry    : angle       0.66503 ( 7539)
  hydrogen bonds       : bond        0.08207 (  227)
  hydrogen bonds       : angle       4.83655 (  526)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.123 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0245
  time to fit residues: 0.7360
Evaluate side-chains
  13 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 3 optimal weight:   20.0000
   chunk 23 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 49 optimal weight:   10.0000
   chunk 50 optimal weight:    7.9990
   chunk 37 optimal weight:    0.6980
   chunk 4 optimal weight:    8.9990
   chunk 38 optimal weight:    9.9990
   chunk 44 optimal weight:    0.0870
   chunk 39 optimal weight:   30.0000
   chunk 32 optimal weight:    8.9990
   overall best weight:    3.7564

-------------------------------------------------------------------------------
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 = 0.3025 r_free = 0.3025 target = 0.043235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.030677 restraints weight = 56779.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.031540 restraints weight = 30876.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.032130 restraints weight = 21059.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.032529 restraints weight = 16254.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.032802 restraints weight = 13609.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.2662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.4884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   5079  Z= 0.188
  Angle     :  0.540   5.122   7539  Z= 0.289
  Chirality :  0.035   0.225   1016
  Planarity :  0.002   0.008    565
  Dihedral  : 23.724 159.949   2323
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 18.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.43 %
    Favored  : 89.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.24 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.42), residues: 441
  helix:  1.56 (0.46), residues: 143
  sheet: -1.53 (1.04), residues: 28
  loop : -1.71 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR F 302 
 PHE   0.000   0.000   PHE A 113 
 TRP   0.000   0.000   TRP F 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 5079)
  covalent geometry    : angle       0.53990 ( 7539)
  hydrogen bonds       : bond        0.06399 (  227)
  hydrogen bonds       : angle       4.26453 (  526)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 879.55 seconds
wall clock time: 15 minutes 49.62 seconds (949.62 seconds total)