Starting phenix.real_space_refine
on Wed Sep 17 06:13:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6b19_7031/09_2025/6b19_7031.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6b19_7031/09_2025/6b19_7031.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6b19_7031/09_2025/6b19_7031.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6b19_7031/09_2025/6b19_7031.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6b19_7031/09_2025/6b19_7031.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6b19_7031/09_2025/6b19_7031.cif"
  }
  resolution = 4.5
  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=   0.001 sd=   0.006
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      37      5.49       5
     C    3032      2.51       5
     N    1054      2.21       5
     O    1167      1.98       5
     H     409      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5699
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 508, 2512
          Classifications: {'peptide': 508}
          Incomplete info: {'truncation_to_alanine': 456}
          Link IDs: {'CIS': 1, 'PTRANS': 33, 'TRANS': 473}
          Chain breaks: 11
          Unresolved chain link angles: 33
          Unresolved non-hydrogen bonds: 1751
          Unresolved non-hydrogen angles: 2259
          Unresolved non-hydrogen dihedrals: 1501
          Unresolved non-hydrogen chiralities: 154
          Planarities with less than four sites: {'GLU:plan': 42, 'GLN:plan1': 34, 'TRP:plan': 17, 'ASN:plan1': 18, 'TYR:plan': 22, 'PHE:plan': 12, 'ARG:plan': 15, 'ASP:plan': 21, 'HIS:plan': 8}
          Unresolved non-hydrogen planarities: 915
    Chain: "B"
      Number of atoms: 1974
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 399, 1974
          Classifications: {'peptide': 399}
          Incomplete info: {'truncation_to_alanine': 363}
          Link IDs: {'PTRANS': 28, 'TRANS': 370}
          Chain breaks: 7
          Unresolved chain link angles: 28
          Unresolved non-hydrogen bonds: 1417
          Unresolved non-hydrogen angles: 1829
          Unresolved non-hydrogen dihedrals: 1227
          Unresolved non-hydrogen chiralities: 120
          Planarities with less than four sites: {'GLU:plan': 35, 'ASP:plan': 18, 'GLN:plan1': 24, 'TRP:plan': 16, 'ASN:plan1': 12, 'PHE:plan': 11, 'ARG:plan': 13, 'HIS:plan': 6, 'TYR:plan': 16}
          Unresolved non-hydrogen planarities: 743
    Chain: "C"
      Number of atoms: 612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 612
          Classifications: {'RNA': 19}
          Modifications used: {'5*END': 1, 'rna3p_pur': 11, 'rna3p_pyr': 7}
          Link IDs: {'rna3p': 18}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 601
          Classifications: {'DNA': 2, 'RNA': 17}
          Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 11}
          Link IDs: {'rna3p': 18}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.07, per 1000 atoms: 0.36
  Number of scatterers: 5699
  At special positions: 0
  Unit cell: (96, 110, 91, 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)
     P      37     15.00
     O    1167      8.00
     N    1054      7.00
     C    3032      6.00
     H     409      1.00
    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: 0.64
  Conformation dependent library (CDL) restraints added in 421.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1716

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 8 sheets defined
      37.3% alpha, 5.4% beta
      19 base pairs and 16 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 44
      removed outlier: 4.276A  pdb=" N   THR A  39 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 83
    Processing helix  chain 'A' and resid 155 through 175
      removed outlier: 3.617A  pdb=" N   ILE A 159 " --> pdb=" O   GLY A 155 " (cutoff:3.500A)
      Proline residue:  A 170  - end of helix
    Processing helix  chain 'A' and resid 196 through 211
      removed outlier: 3.633A  pdb=" N   LYS A 201 " --> pdb=" O   GLN A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 268
    Processing helix  chain 'A' and resid 269 through 271
      No H-bonds generated for 'chain 'A' and resid 269 through 271'
    Processing helix  chain 'A' and resid 276 through 283
      removed outlier: 4.006A  pdb=" N   LEU A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 312
      removed outlier: 3.520A  pdb=" N   LEU A 310 " --> pdb=" O   ASN A 306 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LYS A 311 " --> pdb=" O   ARG A 307 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   GLU A 312 " --> pdb=" O   GLU A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 383
    Processing helix  chain 'A' and resid 394 through 403
    Processing helix  chain 'A' and resid 473 through 489
      removed outlier: 3.699A  pdb=" N   ASP A 488 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 508
      removed outlier: 3.946A  pdb=" N   LEU A 503 " --> pdb=" O   SER A 499 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA A 508 " --> pdb=" O   GLY A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 528
    Processing helix  chain 'A' and resid 545 through 550
    Processing helix  chain 'B' and resid 28 through 45
      removed outlier: 3.680A  pdb=" N   VAL B  35 " --> pdb=" O   ILE B  31 " (cutoff:3.500A)
      removed outlier: 4.916A  pdb=" N   GLU B  36 " --> pdb=" O   LYS B  32 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ILE B  37 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 84
    Processing helix  chain 'B' and resid 84 through 92
      removed outlier: 4.035A  pdb=" N   TRP B  88 " --> pdb=" O   THR B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 118
    Processing helix  chain 'B' and resid 122 through 126
      removed outlier: 4.003A  pdb=" N   LYS B 126 " --> pdb=" O   ASP B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 138
    Processing helix  chain 'B' and resid 154 through 160
    Processing helix  chain 'B' and resid 160 through 175
      Proline residue:  B 170  - end of helix
    Processing helix  chain 'B' and resid 194 through 212
    Processing helix  chain 'B' and resid 253 through 268
    Processing helix  chain 'B' and resid 278 through 283
    Processing helix  chain 'B' and resid 296 through 312
    Processing helix  chain 'B' and resid 363 through 384
    Processing helix  chain 'B' and resid 394 through 402
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48
    Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 180
      removed outlier: 3.545A  pdb=" N   VAL A 179 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 353
      removed outlier: 4.936A  pdb=" N   GLN A 336 " --> pdb=" O   GLN A 332 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLU A 328 " --> pdb=" O   GLN A 340 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   ILE A 329 " --> pdb=" O   LYS A 390 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   PHE A 389 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 441 through 443
    Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 493
    Processing sheet with id=AA6, first strand: chain 'B' and resid 61 through 63
    Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 183
    Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 330
      removed outlier: 6.634A  pdb=" N   ILE B 341 " --> pdb=" O   LEU B 349 " (cutoff:3.500A)

    246 hydrogen bonds defined for protein.
    690 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      52 hydrogen bonds
      104 hydrogen bond angles
      0 basepair planarities
      19 basepair parallelities
      16 stacking parallelities
  Total time for adding SS restraints: 0.89

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        0.75 -     1.20: 409
        1.20 -     1.64: 5362
        1.64 -     2.09: 0
        2.09 -     2.53: 0
        2.53 -     2.98: 1
  Bond restraints: 5772
  Sorted by residual:
  bond pdb=" C   THR A 286 "
       pdb=" N   LEU A 289 "
    ideal  model  delta    sigma   weight residual
    1.329  2.978 -1.649 1.40e-02 5.10e+03 1.39e+04
  bond pdb=" N6    A C 191 "
       pdb=" H61   A C 191 "
    ideal  model  delta    sigma   weight residual
    0.860  0.751  0.109 2.00e-02 2.50e+03 2.98e+01
  bond pdb=" N6    A C 191 "
       pdb=" H62   A C 191 "
    ideal  model  delta    sigma   weight residual
    0.860  0.925 -0.065 2.00e-02 2.50e+03 1.05e+01
  bond pdb=" C1'   A C 191 "
       pdb=" N9    A C 191 "
    ideal  model  delta    sigma   weight residual
    1.475  1.445  0.030 1.50e-02 4.44e+03 3.93e+00
  bond pdb=" C   ILE B 178 "
       pdb=" N   VAL B 179 "
    ideal  model  delta    sigma   weight residual
    1.328  1.282  0.046 2.53e-02 1.56e+03 3.24e+00
  ... (remaining 5767 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    16.28: 8519
       16.28 -    32.56: 0
       32.56 -    48.84: 1
       48.84 -    65.12: 0
       65.12 -    81.40: 1
  Bond angle restraints: 8521
  Sorted by residual:
  angle pdb=" O   THR A 286 "
        pdb=" C   THR A 286 "
        pdb=" N   LEU A 289 "
      ideal   model   delta    sigma   weight residual
     122.59   41.19   81.40 1.33e+00 5.65e-01 3.75e+03
  angle pdb=" CA  THR A 286 "
        pdb=" C   THR A 286 "
        pdb=" N   LEU A 289 "
      ideal   model   delta    sigma   weight residual
     116.84  152.89  -36.05 1.71e+00 3.42e-01 4.45e+02
  angle pdb=" C   ASN A  54 "
        pdb=" N   PRO A  55 "
        pdb=" CA  PRO A  55 "
      ideal   model   delta    sigma   weight residual
     119.84  128.00   -8.16 1.25e+00 6.40e-01 4.26e+01
  angle pdb=" C   THR A 397 "
        pdb=" N   TRP A 398 "
        pdb=" CA  TRP A 398 "
      ideal   model   delta    sigma   weight residual
     120.29  114.26    6.03 1.42e+00 4.96e-01 1.80e+01
  angle pdb=" C   THR A 286 "
        pdb=" N   LEU A 289 "
        pdb=" CA  LEU A 289 "
      ideal   model   delta    sigma   weight residual
     121.70  114.45    7.25 1.80e+00 3.09e-01 1.62e+01
  ... (remaining 8516 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.31: 3152
       29.31 -    58.62: 71
       58.62 -    87.93: 53
       87.93 -   117.24: 2
      117.24 -   146.55: 2
  Dihedral angle restraints: 3280
    sinusoidal: 677
      harmonic: 2603
  Sorted by residual:
  dihedral pdb=" CA  GLU A 413 "
           pdb=" C   GLU A 413 "
           pdb=" N   TRP A 414 "
           pdb=" CA  TRP A 414 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.37  -19.63     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  ASN B 418 "
           pdb=" C   ASN B 418 "
           pdb=" N   THR B 419 "
           pdb=" CA  THR B 419 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.86  -19.14     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  THR A 286 "
           pdb=" C   THR A 286 "
           pdb=" N   LEU A 289 "
           pdb=" CA  LEU A 289 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   18.13  -18.13     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 3277 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 665
       0.039 -    0.078: 250
       0.078 -    0.118: 106
       0.118 -    0.157: 19
       0.157 -    0.196: 3
  Chirality restraints: 1043
  Sorted by residual:
  chirality pdb=" C3'   G C 181 "
            pdb=" C4'   G C 181 "
            pdb=" O3'   G C 181 "
            pdb=" C2'   G C 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.30   -0.20 2.00e-01 2.50e+01 9.59e-01
  chirality pdb=" CA  THR B 240 "
            pdb=" N   THR B 240 "
            pdb=" C   THR B 240 "
            pdb=" CB  THR B 240 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.70   -0.18 2.00e-01 2.50e+01 7.74e-01
  chirality pdb=" CA  LEU B 368 "
            pdb=" N   LEU B 368 "
            pdb=" C   LEU B 368 "
            pdb=" CB  LEU B 368 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.56e-01
  ... (remaining 1040 not shown)

  Planarity restraints: 958
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 286 "   -0.201 2.00e-02 2.50e+03   1.73e-01 2.99e+02
        pdb=" C   THR A 286 "    0.240 2.00e-02 2.50e+03
        pdb=" O   THR A 286 "    0.082 2.00e-02 2.50e+03
        pdb=" N   LEU A 289 "   -0.122 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A  41 "    0.018 2.00e-02 2.50e+03   3.56e-02 1.27e+01
        pdb=" C   MET A  41 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   MET A  41 "    0.023 2.00e-02 2.50e+03
        pdb=" N   GLU A  42 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 296 "   -0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   THR B 296 "    0.059 2.00e-02 2.50e+03
        pdb=" O   THR B 296 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   GLU B 297 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 955 not shown)

  Histogram of nonbonded interaction distances:
        1.78 -     2.34: 282
        2.34 -     2.91: 4305
        2.91 -     3.47: 8362
        3.47 -     4.04: 11082
        4.04 -     4.60: 14332
  Nonbonded interactions: 38363
  Sorted by model distance:
  nonbonded pdb=" H2'   G D  69 "
            pdb=" H8    G D  70 "
     model   vdw
     1.781 2.270
  nonbonded pdb=" H2'   C D  72 "
            pdb=" H8    G D  73 "
     model   vdw
     1.806 2.270
  nonbonded pdb=" H2'   G C 186 "
            pdb=" H6    C C 187 "
     model   vdw
     1.839 2.270
  nonbonded pdb=" H2'   G D  73 "
            pdb=" H6    C D  74 "
     model   vdw
     1.853 2.270
  nonbonded pdb=" H2'   G C 183 "
            pdb=" H8    G C 184 "
     model   vdw
     1.863 2.270
  ... (remaining 38358 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:             0.980
  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:             0.070
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.460
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  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:1.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6326
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      :  0.023   1.649   5363  Z= 1.653
  Angle     :  1.382  81.401   7585  Z= 0.937
  Chirality :  0.048   0.196   1043
  Planarity :  0.008   0.173    925
  Dihedral  : 15.602  74.879   1477
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 16.18
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 19.42 %
    Favored  : 80.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.73 (0.22), residues: 865
  helix: -2.49 (0.24), residues: 298
  sheet: -3.46 (0.48), residues: 95
  loop : -5.02 (0.21), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  56 
 PHE   0.000   0.000   PHE A  61 
 TRP   0.000   0.000   TRP A  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.02326 ( 5363)
  covalent geometry    : angle       1.38220 ( 7585)
  hydrogen bonds       : bond        0.16902 (  298)
  hydrogen bonds       : angle       8.80554 (  794)

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

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

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1730 Ramachandran restraints generated.
    865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.186 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0279
  time to fit residues: 0.7838
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 49 optimal weight:   40.0000
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:   40.0000
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:   30.0000
   chunk 38 optimal weight:   30.0000
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:   20.0000
   chunk 74 optimal weight:   40.0000
   overall best weight:   14.9996

-------------------------------------------------------------------------------
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 = 0.3317 r_free = 0.3317 target = 0.060560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.054122 restraints weight = 140311.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.054521 restraints weight = 114813.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.054791 restraints weight = 98765.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.055038 restraints weight = 88273.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.055191 restraints weight = 80577.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6253
moved from start:          0.4170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   5363  Z= 0.400
  Angle     :  1.045   7.839   7585  Z= 0.594
  Chirality :  0.052   0.324   1043
  Planarity :  0.006   0.031    925
  Dihedral  : 17.003  75.625   1477
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 42.89
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 26.41 %
    Favored  : 73.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

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: -5.68 (0.22), residues: 867
  helix: -2.37 (0.24), residues: 313
  sheet: -3.26 (0.53), residues: 74
  loop : -5.12 (0.21), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  56 
 PHE   0.000   0.000   PHE A  61 
 TRP   0.000   0.000   TRP A  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00625 ( 5363)
  covalent geometry    : angle       1.04530 ( 7585)
  hydrogen bonds       : bond        0.08195 (  298)
  hydrogen bonds       : angle       9.19509 (  794)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.128 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0225
  time to fit residues: 0.6372
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 7 optimal weight:   50.0000
   chunk 49 optimal weight:   30.0000
   chunk 85 optimal weight:   30.0000
   chunk 43 optimal weight:   30.0000
   chunk 22 optimal weight:    0.5980
   chunk 36 optimal weight:    9.9990
   chunk 60 optimal weight:    0.0570
   chunk 5 optimal weight:   20.0000
   chunk 69 optimal weight:    0.9990
   chunk 64 optimal weight:   20.0000
   chunk 38 optimal weight:   20.0000
   overall best weight:    6.3306

-------------------------------------------------------------------------------
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 = 0.3366 r_free = 0.3366 target = 0.061923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.055777 restraints weight = 142822.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.056197 restraints weight = 115807.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.056515 restraints weight = 98777.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.056749 restraints weight = 87107.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.056932 restraints weight = 79084.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6250
moved from start:          0.4163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5363  Z= 0.198
  Angle     :  0.655   5.726   7585  Z= 0.369
  Chirality :  0.043   0.179   1043
  Planarity :  0.003   0.014    925
  Dihedral  : 16.228  74.639   1477
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 21.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.07 %
    Favored  : 79.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    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: -4.69 (0.25), residues: 867
  helix: -1.06 (0.27), residues: 315
  sheet: -3.27 (0.63), residues: 61
  loop : -4.81 (0.22), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  56 
 PHE   0.000   0.000   PHE A  61 
 TRP   0.000   0.000   TRP A  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 5363)
  covalent geometry    : angle       0.65478 ( 7585)
  hydrogen bonds       : bond        0.04852 (  298)
  hydrogen bonds       : angle       7.30538 (  794)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.127 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0255
  time to fit residues: 0.7123
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 50 optimal weight:   40.0000
   chunk 77 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   chunk 52 optimal weight:   30.0000
   chunk 24 optimal weight:   20.0000
   chunk 17 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 66 optimal weight:    7.9990
   chunk 11 optimal weight:   30.0000
   chunk 29 optimal weight:   40.0000
   overall best weight:    6.3990

-------------------------------------------------------------------------------
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 = 0.3352 r_free = 0.3352 target = 0.061383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.055267 restraints weight = 145485.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.055695 restraints weight = 117872.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.056012 restraints weight = 100359.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.056264 restraints weight = 88453.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.056464 restraints weight = 79786.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6268
moved from start:          0.5022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5363  Z= 0.211
  Angle     :  0.675   6.739   7585  Z= 0.378
  Chirality :  0.044   0.190   1043
  Planarity :  0.003   0.015    925
  Dihedral  : 16.408  74.832   1477
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 23.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 25.03 %
    Favored  : 74.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    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: -4.12 (0.27), residues: 867
  helix: -0.30 (0.30), residues: 311
  sheet: -3.25 (0.57), residues: 72
  loop : -4.62 (0.23), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  56 
 PHE   0.000   0.000   PHE A  61 
 TRP   0.000   0.000   TRP A  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 5363)
  covalent geometry    : angle       0.67464 ( 7585)
  hydrogen bonds       : bond        0.05029 (  298)
  hydrogen bonds       : angle       7.00701 (  794)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.195 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0212
  time to fit residues: 0.6147
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 34 optimal weight:   20.0000
   chunk 76 optimal weight:    9.9990
   chunk 37 optimal weight:    9.9990
   chunk 2 optimal weight:    0.0010
   chunk 21 optimal weight:   30.0000
   chunk 42 optimal weight:   40.0000
   chunk 90 optimal weight:   20.0000
   chunk 69 optimal weight:   30.0000
   chunk 73 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 25 optimal weight:   30.0000
   overall best weight:    6.7994

-------------------------------------------------------------------------------
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 = 0.3355 r_free = 0.3355 target = 0.061136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.054995 restraints weight = 147743.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.055398 restraints weight = 120216.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.055719 restraints weight = 102722.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.055958 restraints weight = 90533.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.056145 restraints weight = 81946.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6274
moved from start:          0.5711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5363  Z= 0.203
  Angle     :  0.667   7.112   7585  Z= 0.373
  Chirality :  0.044   0.176   1043
  Planarity :  0.003   0.013    925
  Dihedral  : 16.745  86.319   1477
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 24.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.34 %
    Favored  : 78.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    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: -4.12 (0.27), residues: 867
  helix: -0.34 (0.29), residues: 311
  sheet: -3.23 (0.58), residues: 71
  loop : -4.60 (0.23), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  56 
 PHE   0.000   0.000   PHE A  61 
 TRP   0.000   0.000   TRP A  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 5363)
  covalent geometry    : angle       0.66677 ( 7585)
  hydrogen bonds       : bond        0.04982 (  298)
  hydrogen bonds       : angle       7.09053 (  794)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.178 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0262
  time to fit residues: 0.7032
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 6 optimal weight:   30.0000
   chunk 24 optimal weight:    9.9990
   chunk 44 optimal weight:   30.0000
   chunk 20 optimal weight:   40.0000
   chunk 42 optimal weight:   40.0000
   chunk 64 optimal weight:    6.9990
   chunk 79 optimal weight:    0.0020
   chunk 85 optimal weight:   10.0000
   chunk 82 optimal weight:   50.0000
   chunk 27 optimal weight:   30.0000
   overall best weight:    7.1998

-------------------------------------------------------------------------------
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 = 0.3333 r_free = 0.3333 target = 0.060277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.054247 restraints weight = 144106.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.054658 restraints weight = 116409.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.054982 restraints weight = 98506.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.055217 restraints weight = 86343.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.055396 restraints weight = 78110.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6290
moved from start:          0.6166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5363  Z= 0.213
  Angle     :  0.683   7.094   7585  Z= 0.383
  Chirality :  0.044   0.189   1043
  Planarity :  0.003   0.014    925
  Dihedral  : 16.968  87.333   1477
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 25.39
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 26.87 %
    Favored  : 73.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    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: -4.16 (0.27), residues: 867
  helix: -0.29 (0.30), residues: 304
  sheet: -3.57 (0.54), residues: 79
  loop : -4.57 (0.24), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  56 
 PHE   0.000   0.000   PHE A  61 
 TRP   0.000   0.000   TRP A  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 5363)
  covalent geometry    : angle       0.68270 ( 7585)
  hydrogen bonds       : bond        0.05205 (  298)
  hydrogen bonds       : angle       7.18098 (  794)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.185 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0262
  time to fit residues: 0.7689
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 31 optimal weight:   30.0000
   chunk 72 optimal weight:   40.0000
   chunk 83 optimal weight:   10.0000
   chunk 36 optimal weight:    0.7980
   chunk 25 optimal weight:   50.0000
   chunk 80 optimal weight:   50.0000
   chunk 47 optimal weight:    6.9990
   chunk 76 optimal weight:   10.0000
   chunk 65 optimal weight:    9.9990
   chunk 45 optimal weight:   20.0000
   chunk 79 optimal weight:   30.0000
   overall best weight:    7.5592

-------------------------------------------------------------------------------
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 = 0.3346 r_free = 0.3346 target = 0.060637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.054507 restraints weight = 145663.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.054904 restraints weight = 117664.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.055213 restraints weight = 100383.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.055442 restraints weight = 88450.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.055602 restraints weight = 80087.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6290
moved from start:          0.6521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5363  Z= 0.218
  Angle     :  0.694   7.112   7585  Z= 0.390
  Chirality :  0.044   0.189   1043
  Planarity :  0.003   0.013    925
  Dihedral  : 17.291  95.309   1477
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 26.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 25.72 %
    Favored  : 74.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    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: -4.26 (0.26), residues: 867
  helix: -0.47 (0.29), residues: 310
  sheet: -3.04 (0.66), residues: 60
  loop : -4.69 (0.23), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  56 
 PHE   0.000   0.000   PHE A  61 
 TRP   0.000   0.000   TRP A  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 5363)
  covalent geometry    : angle       0.69414 ( 7585)
  hydrogen bonds       : bond        0.05331 (  298)
  hydrogen bonds       : angle       7.29784 (  794)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.140 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0221
  time to fit residues: 0.6195
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 34 optimal weight:   30.0000
   chunk 19 optimal weight:   50.0000
   chunk 73 optimal weight:    7.9990
   chunk 90 optimal weight:   20.0000
   chunk 70 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 62 optimal weight:   30.0000
   chunk 12 optimal weight:    7.9990
   chunk 42 optimal weight:   40.0000
   chunk 36 optimal weight:    0.0980
   chunk 35 optimal weight:   10.0000
   overall best weight:    6.8190

-------------------------------------------------------------------------------
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 = 0.3337 r_free = 0.3337 target = 0.060537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.054438 restraints weight = 144354.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.054845 restraints weight = 116004.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.055156 restraints weight = 98766.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.055374 restraints weight = 86783.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.055559 restraints weight = 78570.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6285
moved from start:          0.6798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5363  Z= 0.202
  Angle     :  0.656   6.280   7585  Z= 0.368
  Chirality :  0.044   0.177   1043
  Planarity :  0.003   0.013    925
  Dihedral  : 17.350  95.710   1477
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 24.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 26.30 %
    Favored  : 73.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    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: -4.14 (0.27), residues: 867
  helix: -0.28 (0.30), residues: 311
  sheet: -3.58 (0.55), residues: 81
  loop : -4.60 (0.24), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  56 
 PHE   0.000   0.000   PHE A  61 
 TRP   0.000   0.000   TRP A  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 5363)
  covalent geometry    : angle       0.65562 ( 7585)
  hydrogen bonds       : bond        0.04995 (  298)
  hydrogen bonds       : angle       7.08046 (  794)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.190 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0210
  time to fit residues: 0.6109
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 75 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 74 optimal weight:   30.0000
   chunk 84 optimal weight:    4.9990
   chunk 46 optimal weight:   20.0000
   chunk 39 optimal weight:    9.9990
   chunk 31 optimal weight:   40.0000
   chunk 36 optimal weight:   20.0000
   chunk 87 optimal weight:    6.9990
   overall best weight:    5.9990

-------------------------------------------------------------------------------
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 = 0.3707 r_free = 0.3707 target = 0.075061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.061214 restraints weight = 65687.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.061503 restraints weight = 58894.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.061394 restraints weight = 52385.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.061492 restraints weight = 52778.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.061605 restraints weight = 46925.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6844
moved from start:          0.6932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   5363  Z= 0.182
  Angle     :  0.622   5.669   7585  Z= 0.349
  Chirality :  0.043   0.166   1043
  Planarity :  0.003   0.012    925
  Dihedral  : 17.342  97.113   1477
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 22.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 23.76 %
    Favored  : 76.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    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: -3.90 (0.27), residues: 867
  helix: -0.08 (0.30), residues: 314
  sheet: -2.91 (0.68), residues: 62
  loop : -4.58 (0.23), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  56 
 PHE   0.000   0.000   PHE A  61 
 TRP   0.000   0.000   TRP A  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 5363)
  covalent geometry    : angle       0.62246 ( 7585)
  hydrogen bonds       : bond        0.04742 (  298)
  hydrogen bonds       : angle       6.86957 (  794)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.218 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0272
  time to fit residues: 0.7733
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 88 optimal weight:   30.0000
   chunk 2 optimal weight:    7.9990
   chunk 74 optimal weight:   20.0000
   chunk 4 optimal weight:    9.9990
   chunk 12 optimal weight:    7.9990
   chunk 64 optimal weight:    4.9990
   chunk 78 optimal weight:   30.0000
   chunk 45 optimal weight:   40.0000
   chunk 54 optimal weight:   40.0000
   chunk 63 optimal weight:   50.0000
   chunk 28 optimal weight:   20.0000
   overall best weight:   10.1992

-------------------------------------------------------------------------------
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 = 0.3314 r_free = 0.3314 target = 0.059855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.053546 restraints weight = 145952.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.053942 restraints weight = 118389.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.054248 restraints weight = 100423.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.054440 restraints weight = 88212.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.054645 restraints weight = 80131.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6311
moved from start:          0.7434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5363  Z= 0.278
  Angle     :  0.799   6.947   7585  Z= 0.451
  Chirality :  0.047   0.222   1043
  Planarity :  0.004   0.017    925
  Dihedral  : 18.010 102.178   1477
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 32.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 30.10 %
    Favored  : 69.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    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: -4.58 (0.26), residues: 867
  helix: -0.78 (0.29), residues: 298
  sheet: -3.54 (0.60), residues: 66
  loop : -4.72 (0.23), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  56 
 PHE   0.000   0.000   PHE A  61 
 TRP   0.000   0.000   TRP A  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 5363)
  covalent geometry    : angle       0.79882 ( 7585)
  hydrogen bonds       : bond        0.06491 (  298)
  hydrogen bonds       : angle       7.98461 (  794)

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.189 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0266
  time to fit residues: 0.7668
Evaluate side-chains
  10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 10
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 3 optimal weight:   40.0000
   chunk 54 optimal weight:   30.0000
   chunk 23 optimal weight:    0.3980
   chunk 11 optimal weight:   20.0000
   chunk 76 optimal weight:   20.0000
   chunk 41 optimal weight:   30.0000
   chunk 19 optimal weight:   50.0000
   chunk 51 optimal weight:   30.0000
   chunk 60 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0570
   chunk 78 optimal weight:    8.9990
   overall best weight:    6.8906

-------------------------------------------------------------------------------
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 = 0.3690 r_free = 0.3690 target = 0.074401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.061080 restraints weight = 64961.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.061295 restraints weight = 56139.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.061456 restraints weight = 49391.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.061469 restraints weight = 48609.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.061605 restraints weight = 46739.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6766
moved from start:          0.7447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5363  Z= 0.202
  Angle     :  0.667   5.996   7585  Z= 0.376
  Chirality :  0.044   0.179   1043
  Planarity :  0.003   0.013    925
  Dihedral  : 17.628  98.458   1477
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 25.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 26.07 %
    Favored  : 73.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    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: -4.33 (0.27), residues: 867
  helix: -0.40 (0.30), residues: 304
  sheet: -3.23 (0.63), residues: 66
  loop : -4.77 (0.22), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR A  56 
 PHE   0.000   0.000   PHE A  61 
 TRP   0.000   0.000   TRP A  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 5363)
  covalent geometry    : angle       0.66659 ( 7585)
  hydrogen bonds       : bond        0.05159 (  298)
  hydrogen bonds       : angle       7.29137 (  794)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1042.65 seconds
wall clock time: 18 minutes 35.17 seconds (1115.17 seconds total)