Starting phenix.real_space_refine
on Thu Jul 24 10:14:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6b19_7031/07_2025/6b19_7031.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6b19_7031/07_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_7031/07_2025/6b19_7031.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6b19_7031/07_2025/6b19_7031.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6b19_7031/07_2025/6b19_7031.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6b19_7031/07_2025/6b19_7031.cif"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 34, 'HIS:plan': 8, 'TYR:plan': 22, 'ASN:plan1': 18, 'TRP:plan': 17, 'ASP:plan': 21, 'PHE:plan': 12, 'GLU:plan': 42, 'ARG:plan': 15}
          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: {'GLN:plan1': 24, 'HIS:plan': 6, 'TYR:plan': 16, 'ASN:plan1': 12, 'TRP:plan': 16, 'ASP:plan': 18, 'PHE:plan': 11, 'GLU:plan': 35, 'ARG:plan': 13}
          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: 4.53, per 1000 atoms: 0.79
  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: 1.72
  Conformation dependent library (CDL) restraints added in 924.5 milliseconds
  

  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: 2.07
  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: 1.84

  Time building geometry restraints manager: 2.01 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:             0.660
  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:             0.210
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.420
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.650
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.000   0.000   TRP A  24 
 PHE   0.000   0.000   PHE A  61 
 TYR   0.000   0.000   TYR A  56 

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

*********************** 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  : 0.541 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0594
  time to fit residues: 1.8485
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  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    9.9990
   chunk 68 optimal weight:    5.9990
   chunk 38 optimal weight:   30.0000
   chunk 23 optimal weight:    0.0870
   chunk 46 optimal weight:    7.9990
   chunk 36 optimal weight:   20.0000
   chunk 71 optimal weight:    8.9990
   chunk 27 optimal weight:   50.0000
   chunk 43 optimal weight:   40.0000
   chunk 53 optimal weight:   20.0000
   chunk 82 optimal weight:   40.0000
   overall best weight:    6.6166

-------------------------------------------------------------------------------
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 = 0.3397 r_free = 0.3397 target = 0.064000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.057617 restraints weight = 143052.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.058021 restraints weight = 118222.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.058341 restraints weight = 102172.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6144
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5363  Z= 0.217
  Angle     :  0.677   4.706   7585  Z= 0.383
  Chirality :  0.043   0.204   1043
  Planarity :  0.003   0.018    925
  Dihedral  : 15.784  74.692   1477
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 21.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.18 %
    Favored  : 79.82 %
  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 : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.52 (0.25), residues: 867
  helix: -0.86 (0.28), residues: 320
  sheet: -3.68 (0.52), residues: 80
  loop : -4.70 (0.22), residues: 467

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04850 (  298)
  hydrogen bonds       : angle       6.74962 (  794)
  covalent geometry    : bond        0.00337 ( 5363)
  covalent geometry    : angle       0.67691 ( 7585)

*********************** 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  : 0.684 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0920
  time to fit residues: 2.8068
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  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 78 optimal weight:   40.0000
   chunk 79 optimal weight:    9.9990
   chunk 87 optimal weight:   30.0000
   chunk 69 optimal weight:    6.9990
   chunk 86 optimal weight:   20.0000
   chunk 60 optimal weight:    9.9990
   chunk 67 optimal weight:   20.0000
   chunk 84 optimal weight:    6.9990
   chunk 85 optimal weight:    9.9990
   chunk 89 optimal weight:    9.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    8.7990

-------------------------------------------------------------------------------
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 = 0.3343 r_free = 0.3343 target = 0.061258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.055105 restraints weight = 139462.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.055512 restraints weight = 113197.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.055825 restraints weight = 96893.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6227
moved from start:          0.4406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5363  Z= 0.267
  Angle     :  0.783   7.492   7585  Z= 0.441
  Chirality :  0.046   0.239   1043
  Planarity :  0.004   0.016    925
  Dihedral  : 16.457  74.888   1477
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 28.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 23.64 %
    Favored  : 76.36 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.53 (0.25), residues: 867
  helix: -0.84 (0.27), residues: 317
  sheet: -2.82 (0.65), residues: 53
  loop : -4.85 (0.21), residues: 497

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06210 (  298)
  hydrogen bonds       : angle       7.68060 (  794)
  covalent geometry    : bond        0.00420 ( 5363)
  covalent geometry    : angle       0.78285 ( 7585)

*********************** 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  : 0.556 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0534
  time to fit residues: 1.8922
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  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 48 optimal weight:   40.0000
   chunk 51 optimal weight:   40.0000
   chunk 45 optimal weight:   20.0000
   chunk 30 optimal weight:   10.0000
   chunk 58 optimal weight:   10.0000
   chunk 19 optimal weight:   50.0000
   chunk 41 optimal weight:   30.0000
   chunk 13 optimal weight:    9.9990
   chunk 89 optimal weight:    9.9990
   chunk 83 optimal weight:   20.0000
   chunk 0 optimal weight:   30.0000
   overall best weight:   11.9996

-------------------------------------------------------------------------------
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 = 0.059940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.053639 restraints weight = 145003.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.054042 restraints weight = 117728.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.054354 restraints weight = 100356.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6260
moved from start:          0.6070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   5363  Z= 0.328
  Angle     :  0.922   8.497   7585  Z= 0.521
  Chirality :  0.049   0.240   1043
  Planarity :  0.004   0.018    925
  Dihedral  : 17.718  92.830   1477
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 38.55
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 27.22 %
    Favored  : 72.55 %
  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 : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.14 (0.24), residues: 867
  helix: -1.48 (0.27), residues: 290
  sheet: -3.78 (0.53), residues: 74
  loop : -4.86 (0.22), residues: 503

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07309 (  298)
  hydrogen bonds       : angle       8.80847 (  794)
  covalent geometry    : bond        0.00517 ( 5363)
  covalent geometry    : angle       0.92247 ( 7585)

*********************** 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  : 0.534 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0571
  time to fit residues: 1.8813
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  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 50 optimal weight:   30.0000
   chunk 57 optimal weight:   50.0000
   chunk 46 optimal weight:   20.0000
   chunk 44 optimal weight:   30.0000
   chunk 52 optimal weight:   30.0000
   chunk 19 optimal weight:   50.0000
   chunk 11 optimal weight:   30.0000
   chunk 39 optimal weight:   40.0000
   chunk 83 optimal weight:   20.0000
   chunk 61 optimal weight:    0.0980
   chunk 75 optimal weight:    7.9990
   overall best weight:   15.6194

-------------------------------------------------------------------------------
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 = 0.3291 r_free = 0.3291 target = 0.058887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.052467 restraints weight = 142431.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.052837 restraints weight = 116171.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.053111 restraints weight = 100319.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6284
moved from start:          0.7282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   5363  Z= 0.402
  Angle     :  1.065   9.436   7585  Z= 0.596
  Chirality :  0.053   0.243   1043
  Planarity :  0.005   0.021    925
  Dihedral  : 18.748 104.128   1477
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 51.84
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  : 32.99 %
    Favored  : 66.78 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.77 (0.23), residues: 867
  helix: -2.34 (0.25), residues: 280
  sheet: -3.57 (0.63), residues: 54
  loop : -5.06 (0.21), residues: 533

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08645 (  298)
  hydrogen bonds       : angle       9.90648 (  794)
  covalent geometry    : bond        0.00637 ( 5363)
  covalent geometry    : angle       1.06488 ( 7585)

*********************** 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  : 0.657 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0541
  time to fit residues: 1.7745
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  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 38 optimal weight:   50.0000
   chunk 45 optimal weight:   40.0000
   chunk 74 optimal weight:   20.0000
   chunk 20 optimal weight:   40.0000
   chunk 41 optimal weight:   40.0000
   chunk 85 optimal weight:   20.0000
   chunk 55 optimal weight:   30.0000
   chunk 72 optimal weight:   40.0000
   chunk 23 optimal weight:   30.0000
   chunk 73 optimal weight:   20.0000
   overall best weight:   19.9998

-------------------------------------------------------------------------------
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 = 0.3657 r_free = 0.3657 target = 0.073636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.059523 restraints weight = 65881.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.059511 restraints weight = 59256.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.059211 restraints weight = 60591.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6788
moved from start:          0.8451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.048   5363  Z= 0.491
  Angle     :  1.243   9.890   7585  Z= 0.693
  Chirality :  0.057   0.244   1043
  Planarity :  0.007   0.024    925
  Dihedral  : 19.747 109.483   1477
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 66.31
  Ramachandran Plot:
    Outliers :  1.04 %
    Allowed  : 37.83 %
    Favored  : 61.13 %
  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 : 0.97 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.42 (0.22), residues: 867
  helix: -2.95 (0.24), residues: 268
  sheet: -4.71 (0.41), residues: 82
  loop : -5.24 (0.21), residues: 517

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10302 (  298)
  hydrogen bonds       : angle      11.15937 (  794)
  covalent geometry    : bond        0.00780 ( 5363)
  covalent geometry    : angle       1.24316 ( 7585)

*********************** 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  : 0.726 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.1098
  time to fit residues: 3.3742
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  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 87 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 40 optimal weight:   50.0000
   chunk 6 optimal weight:   30.0000
   chunk 36 optimal weight:    5.9990
   chunk 80 optimal weight:   40.0000
   chunk 82 optimal weight:    3.9990
   chunk 34 optimal weight:   20.0000
   chunk 24 optimal weight:   20.0000
   chunk 4 optimal weight:   20.0000
   overall best weight:    6.7992

-------------------------------------------------------------------------------
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 = 0.3689 r_free = 0.3689 target = 0.074737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.061218 restraints weight = 65756.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.061069 restraints weight = 59407.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.060912 restraints weight = 58254.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6778
moved from start:          0.7981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5363  Z= 0.215
  Angle     :  0.760   6.756   7585  Z= 0.426
  Chirality :  0.046   0.182   1043
  Planarity :  0.003   0.016    925
  Dihedral  : 18.372  99.587   1477
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 29.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 27.22 %
    Favored  : 72.78 %
  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 : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.57 (0.23), residues: 867
  helix: -1.94 (0.26), residues: 291
  sheet: -4.13 (0.62), residues: 48
  loop : -5.06 (0.21), residues: 528

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05862 (  298)
  hydrogen bonds       : angle       8.67555 (  794)
  covalent geometry    : bond        0.00341 ( 5363)
  covalent geometry    : angle       0.76023 ( 7585)

*********************** 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  : 0.576 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0565
  time to fit residues: 1.9006
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  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 46 optimal weight:   10.0000
   chunk 25 optimal weight:   20.0000
   chunk 40 optimal weight:   50.0000
   chunk 13 optimal weight:    7.9990
   chunk 71 optimal weight:   30.0000
   chunk 18 optimal weight:   30.0000
   chunk 54 optimal weight:   20.0000
   chunk 63 optimal weight:   40.0000
   chunk 74 optimal weight:   30.0000
   chunk 89 optimal weight:    9.9990
   chunk 70 optimal weight:   30.0000
   overall best weight:   13.5996

-------------------------------------------------------------------------------
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 = 0.3291 r_free = 0.3291 target = 0.059128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.052683 restraints weight = 142044.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.053029 restraints weight = 116451.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.053306 restraints weight = 100425.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6313
moved from start:          0.8425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   5363  Z= 0.364
  Angle     :  0.972   7.707   7585  Z= 0.547
  Chirality :  0.051   0.228   1043
  Planarity :  0.005   0.020    925
  Dihedral  : 19.024 105.691   1477
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 47.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 37.72 %
    Favored  : 62.28 %
  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 : 0.48 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.92 (0.23), residues: 867
  helix: -2.14 (0.27), residues: 278
  sheet: -4.51 (0.49), residues: 62
  loop : -5.23 (0.21), residues: 527

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08085 (  298)
  hydrogen bonds       : angle       9.82952 (  794)
  covalent geometry    : bond        0.00575 ( 5363)
  covalent geometry    : angle       0.97207 ( 7585)

*********************** 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  : 0.605 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0577
  time to fit residues: 1.9666
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  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 4 optimal weight:   20.0000
   chunk 24 optimal weight:   30.0000
   chunk 75 optimal weight:    9.9990
   chunk 88 optimal weight:   30.0000
   chunk 40 optimal weight:   50.0000
   chunk 13 optimal weight:    6.9990
   chunk 74 optimal weight:   30.0000
   chunk 20 optimal weight:   30.0000
   chunk 67 optimal weight:   10.0000
   chunk 56 optimal weight:   30.0000
   chunk 32 optimal weight:   30.0000
   overall best weight:   15.3996

-------------------------------------------------------------------------------
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 = 0.3273 r_free = 0.3273 target = 0.058715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.052265 restraints weight = 140321.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.052617 restraints weight = 115787.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.052884 restraints weight = 99893.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6323
moved from start:          0.8965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   5363  Z= 0.390
  Angle     :  1.035   8.642   7585  Z= 0.584
  Chirality :  0.052   0.236   1043
  Planarity :  0.005   0.023    925
  Dihedral  : 19.444 106.493   1477
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 51.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 37.25 %
    Favored  : 62.75 %
  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 : 0.72 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.15 (0.22), residues: 867
  helix: -2.39 (0.26), residues: 277
  sheet: -4.50 (0.59), residues: 48
  loop : -5.36 (0.20), residues: 542

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08582 (  298)
  hydrogen bonds       : angle      10.51993 (  794)
  covalent geometry    : bond        0.00621 ( 5363)
  covalent geometry    : angle       1.03544 ( 7585)

*********************** 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  : 0.581 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0581
  time to fit residues: 1.9183
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  : 0.575 
-------------------------------------------------------------------------------
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 46 optimal weight:    2.9990
   chunk 28 optimal weight:   50.0000
   chunk 15 optimal weight:   40.0000
   chunk 16 optimal weight:    7.9990
   chunk 42 optimal weight:   50.0000
   chunk 44 optimal weight:   20.0000
   chunk 49 optimal weight:   40.0000
   chunk 27 optimal weight:   30.0000
   chunk 50 optimal weight:   30.0000
   chunk 82 optimal weight:   10.0000
   overall best weight:   14.1996

-------------------------------------------------------------------------------
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 = 0.3281 r_free = 0.3281 target = 0.058932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.052494 restraints weight = 141634.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.052855 restraints weight = 116124.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.053075 restraints weight = 99934.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6308
moved from start:          0.9110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   5363  Z= 0.362
  Angle     :  0.984   8.721   7585  Z= 0.554
  Chirality :  0.051   0.223   1043
  Planarity :  0.005   0.024    925
  Dihedral  : 19.341 105.799   1477
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 47.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 38.52 %
    Favored  : 61.48 %
  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 : 0.60 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.21 (0.23), residues: 867
  helix: -2.41 (0.26), residues: 286
  sheet: -4.92 (0.43), residues: 72
  loop : -5.38 (0.21), residues: 509

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07941 (  298)
  hydrogen bonds       : angle      10.30005 (  794)
  covalent geometry    : bond        0.00577 ( 5363)
  covalent geometry    : angle       0.98355 ( 7585)

********************** 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  : 0.557 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0577
  time to fit residues: 1.8826
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  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 21 optimal weight:   30.0000
   chunk 53 optimal weight:   40.0000
   chunk 86 optimal weight:    9.9990
   chunk 64 optimal weight:    7.9990
   chunk 80 optimal weight:   40.0000
   chunk 90 optimal weight:   10.0000
   chunk 67 optimal weight:   30.0000
   chunk 6 optimal weight:   20.0000
   chunk 27 optimal weight:   30.0000
   chunk 45 optimal weight:   30.0000
   chunk 76 optimal weight:   20.0000
   overall best weight:   13.5996

-------------------------------------------------------------------------------
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 = 0.3276 r_free = 0.3276 target = 0.058740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.052274 restraints weight = 142137.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.052637 restraints weight = 116712.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.052920 restraints weight = 100601.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6318
moved from start:          0.9256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   5363  Z= 0.354
  Angle     :  0.964   8.213   7585  Z= 0.544
  Chirality :  0.051   0.225   1043
  Planarity :  0.005   0.024    925
  Dihedral  : 19.313 106.043   1477
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 48.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 38.18 %
    Favored  : 61.82 %
  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 : 0.48 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.21 (0.22), residues: 867
  helix: -2.35 (0.27), residues: 284
  sheet: -4.82 (0.46), residues: 62
  loop : -5.45 (0.20), residues: 521

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07883 (  298)
  hydrogen bonds       : angle      10.23306 (  794)
  covalent geometry    : bond        0.00565 ( 5363)
  covalent geometry    : angle       0.96354 ( 7585)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2023.66 seconds
wall clock time: 36 minutes 24.72 seconds (2184.72 seconds total)