Starting phenix.real_space_refine
on Fri Aug 22 18:16:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t53_41042/08_2025/8t53_41042.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t53_41042/08_2025/8t53_41042.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t53_41042/08_2025/8t53_41042.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t53_41042/08_2025/8t53_41042.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t53_41042/08_2025/8t53_41042.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t53_41042/08_2025/8t53_41042.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.023
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: 4
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    4418      2.51       5
     N    1094      2.21       5
     O    1110      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6660
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3330
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 398, 3330
          Classifications: {'peptide': 398}
          Link IDs: {'PTRANS': 13, 'TRANS': 384}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 3330
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 398, 3330
          Classifications: {'peptide': 398}
          Link IDs: {'PTRANS': 13, 'TRANS': 384}
          Chain breaks: 5
  Time building chain proxies: 1.49, per 1000 atoms: 0.22
  Number of scatterers: 6660
  At special positions: 0
  Unit cell: (98.8, 113.1, 91, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      38     16.00
     O    1110      8.00
     N    1094      7.00
     C    4418      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.31
  Conformation dependent library (CDL) restraints added in 254.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1528

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 7 sheets defined
      68.8% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 41
      removed outlier: 3.812A  pdb=" N   LEU A  29 " --> pdb=" O   PHE A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 72
      removed outlier: 3.772A  pdb=" N   LEU A  52 " --> pdb=" O   PRO A  48 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   ASP A  53 " --> pdb=" O   GLN A  49 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   THR A  54 " --> pdb=" O   ASP A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 107
    Processing helix  chain 'A' and resid 114 through 142
      Proline residue:  A 129  - end of helix
    Processing helix  chain 'A' and resid 155 through 167
    Processing helix  chain 'A' and resid 168 through 171
    Processing helix  chain 'A' and resid 197 through 204
      removed outlier: 3.593A  pdb=" N   ASN A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 218
      No H-bonds generated for 'chain 'A' and resid 216 through 218'
    Processing helix  chain 'A' and resid 219 through 233
      removed outlier: 3.582A  pdb=" N   THR A 223 " --> pdb=" O   GLU A 219 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   SER A 231 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   HIS A 233 " --> pdb=" O   GLU A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 272
    Processing helix  chain 'A' and resid 273 through 307
      Proline residue:  A 297  - end of helix
    Processing helix  chain 'A' and resid 308 through 310
      No H-bonds generated for 'chain 'A' and resid 308 through 310'
    Processing helix  chain 'A' and resid 322 through 324
      No H-bonds generated for 'chain 'A' and resid 322 through 324'
    Processing helix  chain 'A' and resid 376 through 380
    Processing helix  chain 'A' and resid 381 through 384
    Processing helix  chain 'A' and resid 385 through 393
      removed outlier: 3.625A  pdb=" N   ASN A 389 " --> pdb=" O   PRO A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 413
      removed outlier: 3.844A  pdb=" N   GLU A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   ASP A 413 " --> pdb=" O   ARG A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
      removed outlier: 4.312A  pdb=" N   ALA A 421 " --> pdb=" O   TYR A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 432
      removed outlier: 3.819A  pdb=" N   VAL A 431 " --> pdb=" O   GLY A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 452
    Processing helix  chain 'A' and resid 454 through 471
    Processing helix  chain 'B' and resid 9 through 41
      removed outlier: 3.821A  pdb=" N   LEU B  29 " --> pdb=" O   PHE B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 72
      removed outlier: 4.270A  pdb=" N   THR B  54 " --> pdb=" O   ASP B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 107
    Processing helix  chain 'B' and resid 114 through 142
      Proline residue:  B 129  - end of helix
    Processing helix  chain 'B' and resid 155 through 167
    Processing helix  chain 'B' and resid 168 through 171
      removed outlier: 4.070A  pdb=" N   MET B 171 " --> pdb=" O   GLU B 168 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 168 through 171'
    Processing helix  chain 'B' and resid 196 through 203
      removed outlier: 4.308A  pdb=" N   ILE B 200 " --> pdb=" O   ASP B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 218
      No H-bonds generated for 'chain 'B' and resid 216 through 218'
    Processing helix  chain 'B' and resid 219 through 233
      removed outlier: 3.569A  pdb=" N   THR B 223 " --> pdb=" O   GLU B 219 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   SER B 231 " --> pdb=" O   LEU B 227 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   HIS B 233 " --> pdb=" O   GLU B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 272
    Processing helix  chain 'B' and resid 273 through 307
      Proline residue:  B 297  - end of helix
    Processing helix  chain 'B' and resid 308 through 310
      No H-bonds generated for 'chain 'B' and resid 308 through 310'
    Processing helix  chain 'B' and resid 322 through 324
      No H-bonds generated for 'chain 'B' and resid 322 through 324'
    Processing helix  chain 'B' and resid 376 through 380
    Processing helix  chain 'B' and resid 381 through 384
    Processing helix  chain 'B' and resid 385 through 393
      removed outlier: 3.632A  pdb=" N   ASN B 389 " --> pdb=" O   PRO B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 413
      removed outlier: 3.789A  pdb=" N   GLU B 409 " --> pdb=" O   ASP B 406 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ASP B 413 " --> pdb=" O   ARG B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 421
      removed outlier: 4.321A  pdb=" N   ALA B 421 " --> pdb=" O   TYR B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 427 through 432
      removed outlier: 3.794A  pdb=" N   VAL B 431 " --> pdb=" O   GLY B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 452
    Processing helix  chain 'B' and resid 454 through 471
    Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 188
      removed outlier: 5.839A  pdb=" N   LYS A 147 " --> pdb=" O   ASP A 174 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ILE A 176 " --> pdb=" O   LYS A 147 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   THR A 149 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   PHE A 178 " --> pdb=" O   THR A 149 " (cutoff:3.500A)
      removed outlier: 5.430A  pdb=" N   ILE A 151 " --> pdb=" O   PHE A 178 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   LYS A 148 " --> pdb=" O   HIS A 210 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 148 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ILE A 150 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 314 through 320
    Processing sheet with id=AA3, first strand: chain 'A' and resid 396 through 398
      removed outlier: 6.285A  pdb=" N   LEU A 397 " --> pdb=" O   THR A 426 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 173 through 179
      removed outlier: 7.821A  pdb=" N   ILE B 151 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   PHE B 178 " --> pdb=" O   ILE B 151 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   LYS B 148 " --> pdb=" O   HIS B 210 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   ILE B 212 " --> pdb=" O   LYS B 148 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   ILE B 150 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 188
    Processing sheet with id=AA6, first strand: chain 'B' and resid 314 through 320
    Processing sheet with id=AA7, first strand: chain 'B' and resid 396 through 398
      removed outlier: 6.480A  pdb=" N   LEU B 397 " --> pdb=" O   THR B 426 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7

    382 hydrogen bonds defined for protein.
    1095 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.95

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1993
        1.34 -     1.46: 1641
        1.46 -     1.58: 3154
        1.58 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 6848
  Sorted by residual:
  bond pdb=" CG  GLN B 166 "
       pdb=" CD  GLN B 166 "
    ideal  model  delta    sigma   weight residual
    1.516  1.491  0.025 2.50e-02 1.60e+03 9.64e-01
  bond pdb=" CG  PRO A 328 "
       pdb=" CD  PRO A 328 "
    ideal  model  delta    sigma   weight residual
    1.503  1.473  0.030 3.40e-02 8.65e+02 7.94e-01
  bond pdb=" CB  PRO A 328 "
       pdb=" CG  PRO A 328 "
    ideal  model  delta    sigma   weight residual
    1.492  1.534 -0.042 5.00e-02 4.00e+02 7.11e-01
  bond pdb=" C   SER A 296 "
       pdb=" N   PRO A 297 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.010 1.36e-02 5.41e+03 5.83e-01
  bond pdb=" C   MET B 190 "
       pdb=" N   LEU B 191 "
    ideal  model  delta    sigma   weight residual
    1.331  1.343 -0.011 1.59e-02 3.96e+03 5.13e-01
  ... (remaining 6843 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 9105
        1.78 -     3.57: 141
        3.57 -     5.35: 24
        5.35 -     7.13: 6
        7.13 -     8.91: 2
  Bond angle restraints: 9278
  Sorted by residual:
  angle pdb=" N   VAL B  43 "
        pdb=" CA  VAL B  43 "
        pdb=" C   VAL B  43 "
      ideal   model   delta    sigma   weight residual
     113.42  108.43    4.99 1.17e+00 7.31e-01 1.82e+01
  angle pdb=" CA  PRO A 328 "
        pdb=" N   PRO A 328 "
        pdb=" CD  PRO A 328 "
      ideal   model   delta    sigma   weight residual
     112.00  107.21    4.79 1.40e+00 5.10e-01 1.17e+01
  angle pdb=" N   VAL A  43 "
        pdb=" CA  VAL A  43 "
        pdb=" C   VAL A  43 "
      ideal   model   delta    sigma   weight residual
     113.39  108.57    4.82 1.47e+00 4.63e-01 1.07e+01
  angle pdb=" N   PRO A 328 "
        pdb=" CD  PRO A 328 "
        pdb=" CG  PRO A 328 "
      ideal   model   delta    sigma   weight residual
     103.20   98.55    4.65 1.50e+00 4.44e-01 9.60e+00
  angle pdb=" CA  TRP A 121 "
        pdb=" CB  TRP A 121 "
        pdb=" CG  TRP A 121 "
      ideal   model   delta    sigma   weight residual
     113.60  107.89    5.71 1.90e+00 2.77e-01 9.02e+00
  ... (remaining 9273 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 3578
       16.00 -    32.01: 338
       32.01 -    48.01: 47
       48.01 -    64.01: 5
       64.01 -    80.01: 6
  Dihedral angle restraints: 3974
    sinusoidal: 1622
      harmonic: 2352
  Sorted by residual:
  dihedral pdb=" CA  TRP A 121 "
           pdb=" C   TRP A 121 "
           pdb=" N   THR A 122 "
           pdb=" CA  THR A 122 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.66   21.34     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" CA  GLN B  44 "
           pdb=" C   GLN B  44 "
           pdb=" N   ARG B  45 "
           pdb=" CA  ARG B  45 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.20   18.80     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  GLN A  44 "
           pdb=" C   GLN A  44 "
           pdb=" N   ARG A  45 "
           pdb=" CA  ARG A  45 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.02   17.98     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 3971 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 769
       0.042 -    0.084: 186
       0.084 -    0.126: 64
       0.126 -    0.168: 3
       0.168 -    0.210: 2
  Chirality restraints: 1024
  Sorted by residual:
  chirality pdb=" CA  TRP A 121 "
            pdb=" N   TRP A 121 "
            pdb=" C   TRP A 121 "
            pdb=" CB  TRP A 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CA  TRP B 121 "
            pdb=" N   TRP B 121 "
            pdb=" C   TRP B 121 "
            pdb=" CB  TRP B 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.09e-01
  chirality pdb=" CG  LEU B 125 "
            pdb=" CB  LEU B 125 "
            pdb=" CD1 LEU B 125 "
            pdb=" CD2 LEU B 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 5.14e-01
  ... (remaining 1021 not shown)

  Planarity restraints: 1122
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 327 "   -0.058 5.00e-02 4.00e+02   8.55e-02 1.17e+01
        pdb=" N   PRO A 328 "    0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO A 328 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 328 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 121 "    0.026 2.00e-02 2.50e+03   2.09e-02 1.09e+01
        pdb=" CG  TRP B 121 "   -0.056 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 121 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 121 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 121 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 121 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 121 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 121 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 121 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 121 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 201 "    0.021 2.00e-02 2.50e+03   1.60e-02 6.36e+00
        pdb=" CG  TRP B 201 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 201 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 201 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 201 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 201 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 201 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 201 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 201 "    0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 201 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1119 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 513
        2.74 -     3.28: 7038
        3.28 -     3.82: 11549
        3.82 -     4.36: 12982
        4.36 -     4.90: 21407
  Nonbonded interactions: 53489
  Sorted by model distance:
  nonbonded pdb=" O   PHE A  60 "
            pdb=" OG  SER A  63 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   GLN A  51 "
            pdb=" OG1 THR A  54 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   ALA A 164 "
            pdb=" OG  SER A 167 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   GLN B  51 "
            pdb=" OG1 THR B  54 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   PHE B  60 "
            pdb=" OG  SER B  63 "
     model   vdw
     2.221 3.040
  ... (remaining 53484 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.350
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4588
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      :  0.002   0.042   6848  Z= 0.125
  Angle     :  0.590   8.914   9278  Z= 0.330
  Chirality :  0.041   0.210   1024
  Planarity :  0.005   0.085   1122
  Dihedral  : 12.603  80.013   2446
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  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:  0.81 (0.31), residues: 772
  helix:  0.93 (0.24), residues: 464
  sheet: -0.83 (0.59), residues: 86
  loop :  0.61 (0.45), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  80 
 TYR   0.011   0.001   TYR B  77 
 PHE   0.023   0.002   PHE A  91 
 TRP   0.056   0.002   TRP B 121 
 HIS   0.003   0.001   HIS B 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 6848)
  covalent geometry    : angle       0.59029 ( 9278)
  hydrogen bonds       : bond        0.13381 (  382)
  hydrogen bonds       : angle       6.25662 ( 1095)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 GLU cc_start: 0.7600 (pp20) cc_final: 0.7191 (pp20)
REVERT: B  171 MET cc_start: 0.5928 (ptp) cc_final: 0.5650 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.0584
  time to fit residues: 8.2588
Evaluate side-chains
  81 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0770
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.5344

-------------------------------------------------------------------------------
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 = 0.5064 r_free = 0.5064 target = 0.259132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4850 r_free = 0.4850 target = 0.223120 restraints weight = 23190.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4877 r_free = 0.4877 target = 0.226384 restraints weight = 18213.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4895 r_free = 0.4895 target = 0.228547 restraints weight = 14751.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4907 r_free = 0.4907 target = 0.229981 restraints weight = 12779.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.4917 r_free = 0.4917 target = 0.231255 restraints weight = 11472.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.4851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4794
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   6848  Z= 0.188
  Angle     :  0.621   6.245   9278  Z= 0.336
  Chirality :  0.043   0.186   1024
  Planarity :  0.005   0.055   1122
  Dihedral  :  4.911  21.005    872
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 15.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  5.66 %
    Favored  : 94.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.30), residues: 772
  helix:  1.17 (0.23), residues: 472
  sheet: -0.33 (0.64), residues: 66
  loop :  0.62 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 132 
 TYR   0.015   0.002   TYR A 162 
 PHE   0.029   0.002   PHE A 332 
 TRP   0.046   0.002   TRP A 121 
 HIS   0.006   0.001   HIS B 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 6848)
  covalent geometry    : angle       0.62090 ( 9278)
  hydrogen bonds       : bond        0.04215 (  382)
  hydrogen bonds       : angle       4.84059 ( 1095)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A   79 TYR cc_start: 0.7762 (t80) cc_final: 0.7306 (t80)
REVERT: A   92 ARG cc_start: 0.4788 (tpt170) cc_final: 0.4440 (mmt-90)
REVERT: A  201 TRP cc_start: 0.6240 (m100) cc_final: 0.5381 (m100)
REVERT: B   73 ARG cc_start: 0.2482 (tpt170) cc_final: 0.2158 (tpt170)
  outliers start: 2
  outliers final: 2
  residues processed: 99
  average time/residue: 0.0569
  time to fit residues: 7.8776
Evaluate side-chains
  83 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 81
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 57 optimal weight:    0.0970
   chunk 37 optimal weight:    8.9990
   chunk 0 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0170
   chunk 1 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.7418

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

Flipped N/Q/H residues before XYZ refinement:
A 189 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5102 r_free = 0.5102 target = 0.263857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4870 r_free = 0.4870 target = 0.228755 restraints weight = 23628.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4890 r_free = 0.4890 target = 0.229111 restraints weight = 19649.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4913 r_free = 0.4913 target = 0.231679 restraints weight = 16003.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4919 r_free = 0.4919 target = 0.232604 restraints weight = 13353.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4934 r_free = 0.4934 target = 0.234844 restraints weight = 11995.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.4880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4711
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6848  Z= 0.124
  Angle     :  0.533   5.890   9278  Z= 0.287
  Chirality :  0.041   0.151   1024
  Planarity :  0.004   0.046   1122
  Dihedral  :  4.549  18.907    872
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.31), residues: 772
  helix:  1.42 (0.23), residues: 470
  sheet: -0.18 (0.65), residues: 66
  loop :  0.78 (0.45), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  80 
 TYR   0.019   0.001   TYR A 162 
 PHE   0.029   0.002   PHE A  60 
 TRP   0.033   0.002   TRP A 121 
 HIS   0.002   0.001   HIS B 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6848)
  covalent geometry    : angle       0.53276 ( 9278)
  hydrogen bonds       : bond        0.03738 (  382)
  hydrogen bonds       : angle       4.55532 ( 1095)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A   92 ARG cc_start: 0.4982 (tpt170) cc_final: 0.4669 (mmt-90)
REVERT: A  201 TRP cc_start: 0.6189 (m100) cc_final: 0.4998 (m100)
REVERT: B  150 ILE cc_start: 0.5440 (mm) cc_final: 0.5227 (mm)
REVERT: B  263 MET cc_start: -0.0305 (mmp) cc_final: -0.1362 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0783
  time to fit residues: 10.3912
Evaluate side-chains
  81 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 63 optimal weight:    6.9990
   chunk 17 optimal weight:    0.3980
   chunk 50 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 38 optimal weight:    7.9990
   chunk 67 optimal weight:    6.9990
   chunk 35 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 75 optimal weight:    6.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.5090 r_free = 0.5090 target = 0.262684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4866 r_free = 0.4866 target = 0.228865 restraints weight = 23331.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.4890 r_free = 0.4890 target = 0.229624 restraints weight = 18873.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4911 r_free = 0.4911 target = 0.232078 restraints weight = 15349.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4918 r_free = 0.4918 target = 0.233055 restraints weight = 12974.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4934 r_free = 0.4934 target = 0.235131 restraints weight = 11705.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.4876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4690
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6848  Z= 0.120
  Angle     :  0.521   5.651   9278  Z= 0.282
  Chirality :  0.041   0.161   1024
  Planarity :  0.004   0.046   1122
  Dihedral  :  4.411  18.676    872
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.31), residues: 772
  helix:  1.47 (0.23), residues: 470
  sheet: -0.06 (0.66), residues: 66
  loop :  0.82 (0.46), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 114 
 TYR   0.025   0.001   TYR B 115 
 PHE   0.018   0.001   PHE B 332 
 TRP   0.036   0.002   TRP A 121 
 HIS   0.002   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 6848)
  covalent geometry    : angle       0.52139 ( 9278)
  hydrogen bonds       : bond        0.03528 (  382)
  hydrogen bonds       : angle       4.44979 ( 1095)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  180 ASP cc_start: 0.4553 (t70) cc_final: 0.4312 (t0)
REVERT: A  198 GLU cc_start: 0.7597 (pp20) cc_final: 0.7201 (pp20)
REVERT: A  201 TRP cc_start: 0.6601 (m100) cc_final: 0.5342 (m100)
REVERT: B  263 MET cc_start: -0.0158 (mmp) cc_final: -0.1167 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.0701
  time to fit residues: 9.8363
Evaluate side-chains
  82 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 43 optimal weight:    0.1980
   chunk 35 optimal weight:    1.9990
   chunk 59 optimal weight:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 189 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5070 r_free = 0.5070 target = 0.262864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4876 r_free = 0.4876 target = 0.232328 restraints weight = 24214.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4879 r_free = 0.4879 target = 0.232965 restraints weight = 20207.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4914 r_free = 0.4914 target = 0.235552 restraints weight = 17151.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.235790 restraints weight = 15003.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4917 r_free = 0.4917 target = 0.236916 restraints weight = 12761.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.4877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4641
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6848  Z= 0.124
  Angle     :  0.512   5.813   9278  Z= 0.279
  Chirality :  0.041   0.222   1024
  Planarity :  0.004   0.040   1122
  Dihedral  :  4.377  18.740    872
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.31), residues: 772
  helix:  1.48 (0.23), residues: 472
  sheet: -0.12 (0.65), residues: 66
  loop :  0.89 (0.47), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  55 
 TYR   0.022   0.001   TYR A 162 
 PHE   0.028   0.001   PHE B  60 
 TRP   0.039   0.002   TRP A 121 
 HIS   0.003   0.001   HIS B 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 6848)
  covalent geometry    : angle       0.51206 ( 9278)
  hydrogen bonds       : bond        0.03477 (  382)
  hydrogen bonds       : angle       4.41120 ( 1095)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 TYR cc_start: 0.7894 (t80) cc_final: 0.7541 (t80)
REVERT: A   92 ARG cc_start: 0.4880 (tpt170) cc_final: 0.4481 (mmt-90)
REVERT: A  171 MET cc_start: 0.7154 (mtt) cc_final: 0.6845 (mtt)
REVERT: A  198 GLU cc_start: 0.7330 (pp20) cc_final: 0.6928 (pp20)
REVERT: A  201 TRP cc_start: 0.6372 (m100) cc_final: 0.5071 (m100)
REVERT: B  190 MET cc_start: 0.7243 (ttt) cc_final: 0.6980 (ttt)
REVERT: B  263 MET cc_start: -0.0164 (mmp) cc_final: -0.1245 (mmm)
REVERT: B  290 MET cc_start: 0.4532 (mmt) cc_final: 0.4323 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.0802
  time to fit residues: 11.8086
Evaluate side-chains
  88 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    0.0970
   chunk 60 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 38 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5033 r_free = 0.5033 target = 0.256279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4817 r_free = 0.4817 target = 0.223515 restraints weight = 24055.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.4838 r_free = 0.4838 target = 0.222948 restraints weight = 19467.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4850 r_free = 0.4850 target = 0.224436 restraints weight = 15983.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4872 r_free = 0.4872 target = 0.226705 restraints weight = 13674.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4877 r_free = 0.4877 target = 0.227901 restraints weight = 11958.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.4824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4880
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.116   6848  Z= 0.180
  Angle     :  0.624   7.098   9278  Z= 0.340
  Chirality :  0.044   0.164   1024
  Planarity :  0.004   0.041   1122
  Dihedral  :  5.011  21.305    872
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 15.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.31), residues: 772
  helix:  1.14 (0.23), residues: 472
  sheet: -0.43 (0.62), residues: 66
  loop :  0.42 (0.46), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  45 
 TYR   0.021   0.002   TYR A 162 
 PHE   0.021   0.002   PHE B 332 
 TRP   0.042   0.002   TRP A 121 
 HIS   0.005   0.001   HIS B 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 6848)
  covalent geometry    : angle       0.62390 ( 9278)
  hydrogen bonds       : bond        0.03846 (  382)
  hydrogen bonds       : angle       4.59186 ( 1095)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 ARG cc_start: 0.4762 (tpt170) cc_final: 0.4317 (mmt-90)
REVERT: A  198 GLU cc_start: 0.7527 (pp20) cc_final: 0.7297 (pp20)
REVERT: A  201 TRP cc_start: 0.6469 (m100) cc_final: 0.5481 (m100)
REVERT: B   79 TYR cc_start: 0.7939 (t80) cc_final: 0.7729 (t80)
REVERT: B  121 TRP cc_start: 0.6588 (m-90) cc_final: 0.6185 (m-90)
REVERT: B  263 MET cc_start: 0.0005 (mmp) cc_final: -0.1094 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0714
  time to fit residues: 10.8929
Evaluate side-chains
  92 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0770
   chunk 36 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 46 optimal weight:    0.6980
   chunk 41 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.5938

-------------------------------------------------------------------------------
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 = 0.5069 r_free = 0.5069 target = 0.263010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4857 r_free = 0.4857 target = 0.229392 restraints weight = 23753.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4888 r_free = 0.4888 target = 0.230832 restraints weight = 19574.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4905 r_free = 0.4905 target = 0.232901 restraints weight = 16043.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4913 r_free = 0.4913 target = 0.234059 restraints weight = 13589.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4924 r_free = 0.4924 target = 0.235316 restraints weight = 12125.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.4873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4712
moved from start:          0.3317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055   6848  Z= 0.116
  Angle     :  0.551   6.190   9278  Z= 0.295
  Chirality :  0.042   0.180   1024
  Planarity :  0.004   0.041   1122
  Dihedral  :  4.565  18.820    872
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.31), residues: 772
  helix:  1.40 (0.23), residues: 470
  sheet: -0.18 (0.64), residues: 66
  loop :  0.65 (0.46), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  80 
 TYR   0.016   0.001   TYR A 162 
 PHE   0.018   0.001   PHE A 107 
 TRP   0.035   0.002   TRP A 121 
 HIS   0.013   0.001   HIS A  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6848)
  covalent geometry    : angle       0.55137 ( 9278)
  hydrogen bonds       : bond        0.03497 (  382)
  hydrogen bonds       : angle       4.44844 ( 1095)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 ARG cc_start: 0.4914 (tpt170) cc_final: 0.4675 (mmt-90)
REVERT: A  147 LYS cc_start: 0.7019 (pttt) cc_final: 0.6665 (pttt)
REVERT: A  201 TRP cc_start: 0.6404 (m100) cc_final: 0.5345 (m100)
REVERT: B  121 TRP cc_start: 0.6554 (m-90) cc_final: 0.6056 (m-90)
REVERT: B  170 MET cc_start: 0.1780 (mmt) cc_final: 0.1548 (mmt)
REVERT: B  171 MET cc_start: 0.6633 (ptp) cc_final: 0.6405 (ptp)
REVERT: B  263 MET cc_start: -0.0157 (mmp) cc_final: -0.1195 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0602
  time to fit residues: 9.3164
Evaluate side-chains
  98 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0570
   chunk 22 optimal weight:    0.9980
   chunk 9 optimal weight:    7.9990
   chunk 1 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.7698

-------------------------------------------------------------------------------
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 = 0.5334 r_free = 0.5334 target = 0.314515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.5310 r_free = 0.5310 target = 0.304755 restraints weight = 30657.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.5318 r_free = 0.5318 target = 0.305711 restraints weight = 20581.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.5327 r_free = 0.5327 target = 0.306510 restraints weight = 15405.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.5331 r_free = 0.5331 target = 0.306909 restraints weight = 11941.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.5336 r_free = 0.5336 target = 0.307383 restraints weight = 9972.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.5006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4193
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6848  Z= 0.124
  Angle     :  0.561   6.401   9278  Z= 0.299
  Chirality :  0.042   0.177   1024
  Planarity :  0.004   0.035   1122
  Dihedral  :  4.547  18.973    872
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.31), residues: 772
  helix:  1.41 (0.23), residues: 472
  sheet: -0.08 (0.66), residues: 66
  loop :  0.71 (0.47), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  80 
 TYR   0.030   0.002   TYR B  77 
 PHE   0.015   0.001   PHE A  46 
 TRP   0.038   0.002   TRP A 121 
 HIS   0.008   0.001   HIS A  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6848)
  covalent geometry    : angle       0.56056 ( 9278)
  hydrogen bonds       : bond        0.03493 (  382)
  hydrogen bonds       : angle       4.43102 ( 1095)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 ARG cc_start: 0.5398 (tpt170) cc_final: 0.4883 (mmt-90)
REVERT: A  147 LYS cc_start: 0.6533 (pttt) cc_final: 0.6305 (pttt)
REVERT: B  121 TRP cc_start: 0.6061 (m-90) cc_final: 0.5679 (m-90)
REVERT: B  263 MET cc_start: -0.0335 (mmp) cc_final: -0.1269 (mmm)
REVERT: B  290 MET cc_start: 0.5847 (ptm) cc_final: 0.5478 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0586
  time to fit residues: 8.5717
Evaluate side-chains
  97 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 26 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 54 optimal weight:    0.2980
   chunk 2 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0980
   chunk 76 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 386 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5068 r_free = 0.5068 target = 0.263291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4877 r_free = 0.4877 target = 0.231505 restraints weight = 23732.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4872 r_free = 0.4872 target = 0.233069 restraints weight = 19217.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4917 r_free = 0.4917 target = 0.236040 restraints weight = 16362.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.236206 restraints weight = 14279.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.236356 restraints weight = 13293.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.4867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4668
moved from start:          0.3744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6848  Z= 0.113
  Angle     :  0.557   6.488   9278  Z= 0.293
  Chirality :  0.042   0.168   1024
  Planarity :  0.003   0.034   1122
  Dihedral  :  4.406  18.493    872
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.31), residues: 772
  helix:  1.46 (0.23), residues: 474
  sheet:  0.03 (0.66), residues: 66
  loop :  0.69 (0.47), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  80 
 TYR   0.017   0.001   TYR A 162 
 PHE   0.016   0.001   PHE A 107 
 TRP   0.040   0.002   TRP A 121 
 HIS   0.006   0.001   HIS A  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 6848)
  covalent geometry    : angle       0.55687 ( 9278)
  hydrogen bonds       : bond        0.03398 (  382)
  hydrogen bonds       : angle       4.36200 ( 1095)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 ARG cc_start: 0.4925 (tpt170) cc_final: 0.4688 (mmt-90)
REVERT: A  147 LYS cc_start: 0.6561 (pttt) cc_final: 0.6356 (pttp)
REVERT: B   79 TYR cc_start: 0.7904 (t80) cc_final: 0.7537 (t80)
REVERT: B  121 TRP cc_start: 0.6647 (m-90) cc_final: 0.6066 (m-90)
REVERT: B  263 MET cc_start: -0.0037 (mmp) cc_final: -0.1064 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.0532
  time to fit residues: 8.3817
Evaluate side-chains
  103 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 67 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0670
   chunk 27 optimal weight:    0.1980
   chunk 20 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 4 optimal weight:    0.2980
   overall best weight:    0.3518

-------------------------------------------------------------------------------
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 = 0.5093 r_free = 0.5093 target = 0.265878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4946 r_free = 0.4946 target = 0.239047 restraints weight = 23599.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.238361 restraints weight = 19885.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4936 r_free = 0.4936 target = 0.240114 restraints weight = 17201.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4944 r_free = 0.4944 target = 0.241249 restraints weight = 14044.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4953 r_free = 0.4953 target = 0.242276 restraints weight = 12628.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.4912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4505
moved from start:          0.3840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6848  Z= 0.107
  Angle     :  0.560   7.197   9278  Z= 0.292
  Chirality :  0.041   0.200   1024
  Planarity :  0.003   0.034   1122
  Dihedral  :  4.228  17.673    872
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.31), residues: 772
  helix:  1.79 (0.23), residues: 462
  sheet:  0.28 (0.69), residues: 66
  loop :  0.47 (0.46), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  80 
 TYR   0.022   0.001   TYR B  77 
 PHE   0.028   0.001   PHE A  91 
 TRP   0.024   0.002   TRP B 201 
 HIS   0.007   0.001   HIS A  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 6848)
  covalent geometry    : angle       0.56031 ( 9278)
  hydrogen bonds       : bond        0.03377 (  382)
  hydrogen bonds       : angle       4.26701 ( 1095)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 ARG cc_start: 0.5063 (tpt170) cc_final: 0.4707 (mmt-90)
REVERT: B   79 TYR cc_start: 0.7498 (t80) cc_final: 0.6689 (t80)
REVERT: B  121 TRP cc_start: 0.6584 (m-90) cc_final: 0.6158 (m-90)
REVERT: B  136 LYS cc_start: 0.6547 (pttp) cc_final: 0.6207 (pttm)
REVERT: B  212 ILE cc_start: 0.7298 (mm) cc_final: 0.7091 (mm)
REVERT: B  263 MET cc_start: -0.0009 (mmp) cc_final: -0.1048 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0649
  time to fit residues: 9.9663
Evaluate side-chains
  102 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 3 optimal weight:    0.0970
   chunk 65 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0050
   chunk 70 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.4592

-------------------------------------------------------------------------------
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 = 0.5091 r_free = 0.5091 target = 0.265294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4989 r_free = 0.4989 target = 0.243173 restraints weight = 23338.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4929 r_free = 0.4929 target = 0.241902 restraints weight = 18290.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4945 r_free = 0.4945 target = 0.243052 restraints weight = 16123.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4947 r_free = 0.4947 target = 0.243220 restraints weight = 14177.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4949 r_free = 0.4949 target = 0.243409 restraints weight = 13367.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.4918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4432
moved from start:          0.3998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6848  Z= 0.107
  Angle     :  0.549   6.653   9278  Z= 0.287
  Chirality :  0.042   0.178   1024
  Planarity :  0.003   0.034   1122
  Dihedral  :  4.174  17.608    872
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.87 (0.31), residues: 772
  helix:  1.86 (0.23), residues: 462
  sheet:  0.26 (0.68), residues: 66
  loop :  0.47 (0.46), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  80 
 TYR   0.012   0.001   TYR B 162 
 PHE   0.023   0.001   PHE A  91 
 TRP   0.029   0.002   TRP A 121 
 HIS   0.006   0.001   HIS A  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 6848)
  covalent geometry    : angle       0.54941 ( 9278)
  hydrogen bonds       : bond        0.03280 (  382)
  hydrogen bonds       : angle       4.21447 ( 1095)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1440.99 seconds
wall clock time: 25 minutes 28.39 seconds (1528.39 seconds total)