Starting phenix.real_space_refine
on Fri Aug 22 21:01:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gf8_51311/08_2025/9gf8_51311.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gf8_51311/08_2025/9gf8_51311.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gf8_51311/08_2025/9gf8_51311.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gf8_51311/08_2025/9gf8_51311.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gf8_51311/08_2025/9gf8_51311.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gf8_51311/08_2025/9gf8_51311.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.000
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
     S      35      5.16       5
     C    2562      2.51       5
     N     648      2.21       5
     O     683      1.98       5
     H    3965      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7893
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6063
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 387, 6063
          Classifications: {'peptide': 387}
          Link IDs: {'PTRANS': 16, 'TRANS': 370}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 1830
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
  Time building chain proxies: 1.65, per 1000 atoms: 0.21
  Number of scatterers: 7893
  At special positions: 0
  Unit cell: (61.336, 87.516, 103.224, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      35     16.00
     O     683      8.00
     N     648      7.00
     C    2562      6.00
     H    3965      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.69
  Conformation dependent library (CDL) restraints added in 288.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  914

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 3 sheets defined
      69.7% alpha, 12.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 99 through 132
      removed outlier: 4.179A  pdb=" N   VAL A 103 " --> pdb=" O   PHE A  99 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   VAL A 104 " --> pdb=" O   GLY A 100 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   PHE A 105 " --> pdb=" O   TRP A 101 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   GLY A 122 " --> pdb=" O   HIS A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 144
      removed outlier: 3.855A  pdb=" N   ALA A 144 " --> pdb=" O   GLU A 140 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 140 through 144'
    Processing helix  chain 'A' and resid 145 through 169
      removed outlier: 3.896A  pdb=" N   MET A 151 " --> pdb=" O   GLY A 147 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ILE A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   PHE A 155 " --> pdb=" O   MET A 151 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   SER A 158 " --> pdb=" O   ILE A 154 " (cutoff:3.500A)
      Proline residue:  A 159  - end of helix
      removed outlier: 4.396A  pdb=" N   ILE A 163 " --> pdb=" O   PRO A 159 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   PHE A 164 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ASP A 166 " --> pdb=" O   SER A 162 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ARG A 167 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 188
      removed outlier: 3.943A  pdb=" N   ALA A 178 " --> pdb=" O   ALA A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 203
    Processing helix  chain 'A' and resid 206 through 214
      removed outlier: 3.640A  pdb=" N   GLN A 214 " --> pdb=" O   SER A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 222
      removed outlier: 3.516A  pdb=" N   VAL A 218 " --> pdb=" O   GLN A 214 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   LEU A 220 " --> pdb=" O   SER A 216 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   GLY A 221 " --> pdb=" O   LEU A 217 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   HIS A 222 " --> pdb=" O   VAL A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 254
      Proline residue:  A 247  - end of helix
    Processing helix  chain 'A' and resid 258 through 277
      removed outlier: 5.080A  pdb=" N   GLN A 264 " --> pdb=" O   ALA A 260 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   VAL A 265 " --> pdb=" O   GLN A 261 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU A 266 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   SER A 267 " --> pdb=" O   PHE A 263 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   THR A 268 " --> pdb=" O   GLN A 264 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   PHE A 269 " --> pdb=" O   VAL A 265 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   MET A 270 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 280
      No H-bonds generated for 'chain 'A' and resid 278 through 280'
    Processing helix  chain 'A' and resid 312 through 317
      removed outlier: 4.209A  pdb=" N   VAL A 315 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 333
      removed outlier: 3.693A  pdb=" N   TRP A 324 " --> pdb=" O   THR A 320 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   LEU A 333 " --> pdb=" O   ALA A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 341
      removed outlier: 3.596A  pdb=" N   TYR A 339 " --> pdb=" O   TYR A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 347
      removed outlier: 4.084A  pdb=" N   VAL A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 378
      removed outlier: 3.807A  pdb=" N   LEU A 359 " --> pdb=" O   GLU A 355 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   HIS A 376 " --> pdb=" O   LEU A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 385
    Processing helix  chain 'A' and resid 386 through 404
      removed outlier: 3.876A  pdb=" N   GLN A 390 " --> pdb=" O   LYS A 386 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 429
      removed outlier: 4.075A  pdb=" N   GLY A 425 " --> pdb=" O   GLY A 421 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   PHE A 426 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE A 427 " --> pdb=" O   CYS A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 440
      removed outlier: 3.531A  pdb=" N   ILE A 434 " --> pdb=" O   ILE A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 455
      removed outlier: 3.666A  pdb=" N   MET A 454 " --> pdb=" O   TYR A 450 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   MET A 455 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 461
    Processing helix  chain 'A' and resid 461 through 474
      removed outlier: 4.091A  pdb=" N   ASN A 471 " --> pdb=" O   GLY A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 484
      removed outlier: 4.085A  pdb=" N   TYR A 481 " --> pdb=" O   HIS A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 495
      removed outlier: 3.575A  pdb=" N   ILE A 488 " --> pdb=" O   GLY A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 508
    Processing helix  chain 'A' and resid 509 through 511
      No H-bonds generated for 'chain 'A' and resid 509 through 511'
    Processing helix  chain 'B' and resid 30 through 35
    Processing helix  chain 'B' and resid 91 through 95
    Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 7
      removed outlier: 3.625A  pdb=" N   GLN B   5 " --> pdb=" O   SER B  27 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   THR B  25 " --> pdb=" O   GLN B   7 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   SER B  84 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 14
      removed outlier: 3.675A  pdb=" N   HIS B 101 " --> pdb=" O   GLY B  40 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   MET B  39 " --> pdb=" O   ALA B  55 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   ALA B  55 " --> pdb=" O   MET B  39 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   TRP B  41 " --> pdb=" O   VAL B  53 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 12 through 14

    238 hydrogen bonds defined for protein.
    672 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: 1.71

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3953
        1.03 -     1.23: 12
        1.23 -     1.42: 1710
        1.42 -     1.61: 2254
        1.61 -     1.81: 58
  Bond restraints: 7987
  Sorted by residual:
  bond pdb=" N   VAL B   4 "
       pdb=" CA  VAL B   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.01e+00
  bond pdb=" N   VAL B   4 "
       pdb=" H   VAL B   4 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.26e+00
  bond pdb=" N   GLY A 116 "
       pdb=" CA  GLY A 116 "
    ideal  model  delta    sigma   weight residual
    1.454  1.447  0.007 1.24e-02 6.50e+03 2.98e-01
  bond pdb=" CA  ILE A 404 "
       pdb=" CB  ILE A 404 "
    ideal  model  delta    sigma   weight residual
    1.539  1.536  0.003 5.40e-03 3.43e+04 2.86e-01
  bond pdb=" CB  PRO A 487 "
       pdb=" CG  PRO A 487 "
    ideal  model  delta    sigma   weight residual
    1.492  1.465  0.027 5.00e-02 4.00e+02 2.82e-01
  ... (remaining 7982 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.05: 13525
        1.05 -     2.10: 841
        2.10 -     3.15: 16
        3.15 -     4.20: 12
        4.20 -     5.25: 4
  Bond angle restraints: 14398
  Sorted by residual:
  angle pdb=" CA  VAL B   4 "
        pdb=" N   VAL B   4 "
        pdb=" H   VAL B   4 "
      ideal   model   delta    sigma   weight residual
     114.00  109.48    4.52 3.00e+00 1.11e-01 2.27e+00
  angle pdb=" CA  TYR A 125 "
        pdb=" CB  TYR A 125 "
        pdb=" CG  TYR A 125 "
      ideal   model   delta    sigma   weight residual
     113.90  111.32    2.58 1.80e+00 3.09e-01 2.05e+00
  angle pdb=" C   GLU A 349 "
        pdb=" CA  GLU A 349 "
        pdb=" CB  GLU A 349 "
      ideal   model   delta    sigma   weight residual
     110.65  107.90    2.75 1.95e+00 2.63e-01 1.99e+00
  angle pdb=" N   GLU A 349 "
        pdb=" CA  GLU A 349 "
        pdb=" CB  GLU A 349 "
      ideal   model   delta    sigma   weight residual
     113.65  111.72    1.93 1.47e+00 4.63e-01 1.73e+00
  angle pdb=" C   PRO A 486 "
        pdb=" N   PRO A 487 "
        pdb=" CD  PRO A 487 "
      ideal   model   delta    sigma   weight residual
     125.00  130.25   -5.25 4.10e+00 5.95e-02 1.64e+00
  ... (remaining 14393 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 3501
       17.89 -    35.78: 156
       35.78 -    53.68: 81
       53.68 -    71.57: 26
       71.57 -    89.46: 6
  Dihedral angle restraints: 3770
    sinusoidal: 2006
      harmonic: 1764
  Sorted by residual:
  dihedral pdb=" CA  GLU A 348 "
           pdb=" C   GLU A 348 "
           pdb=" N   GLU A 349 "
           pdb=" CA  GLU A 349 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.47   17.53     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" N   GLU A 437 "
           pdb=" CA  GLU A 437 "
           pdb=" CB  GLU A 437 "
           pdb=" CG  GLU A 437 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.13  -57.87     3      1.50e+01 4.44e-03 9.45e+00
  dihedral pdb=" CA  ARG A 506 "
           pdb=" CB  ARG A 506 "
           pdb=" CG  ARG A 506 "
           pdb=" CD  ARG A 506 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  124.90   55.10     3      1.50e+01 4.44e-03 9.33e+00
  ... (remaining 3767 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 413
       0.029 -    0.057: 128
       0.057 -    0.086: 45
       0.086 -    0.114: 20
       0.114 -    0.143: 6
  Chirality restraints: 612
  Sorted by residual:
  chirality pdb=" CA  ILE A 353 "
            pdb=" N   ILE A 353 "
            pdb=" C   ILE A 353 "
            pdb=" CB  ILE A 353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.09e-01
  chirality pdb=" CA  VAL B   4 "
            pdb=" N   VAL B   4 "
            pdb=" C   VAL B   4 "
            pdb=" CB  VAL B   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.25e-01
  chirality pdb=" CA  VAL A 497 "
            pdb=" N   VAL A 497 "
            pdb=" C   VAL A 497 "
            pdb=" CB  VAL A 497 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.99e-01
  ... (remaining 609 not shown)

  Planarity restraints: 1167
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 337 "    0.015 5.00e-02 4.00e+02   2.29e-02 8.39e-01
        pdb=" N   PRO A 338 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO A 338 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO A 338 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 462 "    0.014 5.00e-02 4.00e+02   2.06e-02 6.76e-01
        pdb=" N   PRO A 463 "   -0.036 5.00e-02 4.00e+02
        pdb=" CA  PRO A 463 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO A 463 "    0.011 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 198 "   -0.009 2.00e-02 2.50e+03   4.45e-03 5.94e-01
        pdb=" CG  TYR A 198 "    0.012 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 198 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 198 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 198 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 198 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 198 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 198 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD1 TYR A 198 "    0.001 2.00e-02 2.50e+03
        pdb=" HD2 TYR A 198 "    0.000 2.00e-02 2.50e+03
        pdb=" HE1 TYR A 198 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE2 TYR A 198 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1164 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 430
        2.20 -     2.80: 16114
        2.80 -     3.40: 21178
        3.40 -     4.00: 26496
        4.00 -     4.60: 41416
  Nonbonded interactions: 105634
  Sorted by model distance:
  nonbonded pdb=" H   GLY B  17 "
            pdb=" O   LEU B  90 "
     model   vdw
     1.605 2.450
  nonbonded pdb=" H   SER B  57 "
            pdb=" O   ASN B  61 "
     model   vdw
     1.648 2.450
  nonbonded pdb=" OE1 GLU B   8 "
            pdb=" H   GLU B   8 "
     model   vdw
     1.659 2.450
  nonbonded pdb=" OE2 GLU A  96 "
            pdb="HH11 ARG A 226 "
     model   vdw
     1.691 2.450
  nonbonded pdb=" H   LYS B  91 "
            pdb=" OD2 ASP B  94 "
     model   vdw
     1.702 2.450
  ... (remaining 105629 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:             2.020
  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:             0.050
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.460
  Find NCS groups from input model:        0.020
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6600
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   0.033   4022  Z= 0.099
  Angle     :  0.424   5.250   5442  Z= 0.229
  Chirality :  0.036   0.143    612
  Planarity :  0.003   0.023    682
  Dihedral  : 10.775  89.461   1424
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  4.08 %
    Favored  : 94.96 %
  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:  0.32 (0.40), residues: 500
  helix:  0.46 (0.32), residues: 290
  sheet: -0.63 (0.71), residues: 49
  loop :  0.36 (0.54), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 371 
 TYR   0.012   0.001   TYR A 198 
 PHE   0.006   0.001   PHE A 182 
 TRP   0.007   0.001   TRP A 324 
 HIS   0.002   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 4022)
  covalent geometry    : angle       0.42427 ( 5442)
  hydrogen bonds       : bond        0.19948 (  231)
  hydrogen bonds       : angle       7.48418 (  672)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 131
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 MET cc_start: 0.4064 (ttp) cc_final: 0.3824 (tmm)
REVERT: A  210 SER cc_start: 0.8776 (t) cc_final: 0.8573 (t)
REVERT: A  419 PHE cc_start: 0.8704 (m-10) cc_final: 0.8294 (m-10)
REVERT: A  420 LEU cc_start: 0.8926 (tp) cc_final: 0.8647 (tt)
  outliers start: 4
  outliers final: 2
  residues processed: 134
  average time/residue: 0.1832
  time to fit residues: 29.7142
Evaluate side-chains
  102 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  335 TYR
Chi-restraints excluded: chain A residue  471 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.4980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 232 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.189009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.138200 restraints weight = 16690.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.144549 restraints weight = 6609.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.148395 restraints weight = 3976.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.150570 restraints weight = 3024.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.151345 restraints weight = 2617.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4022  Z= 0.146
  Angle     :  0.532   5.342   5442  Z= 0.290
  Chirality :  0.038   0.139    612
  Planarity :  0.006   0.104    682
  Dihedral  :  5.155  52.090    554
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 13.19 %
    Favored  : 85.85 %
  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:  0.20 (0.39), residues: 500
  helix:  0.37 (0.31), residues: 302
  sheet: -0.56 (0.71), residues: 49
  loop :  0.24 (0.57), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 371 
 TYR   0.012   0.001   TYR A 198 
 PHE   0.010   0.001   PHE A 205 
 TRP   0.009   0.001   TRP A 324 
 HIS   0.002   0.001   HIS A 376 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4022)
  covalent geometry    : angle       0.53190 ( 5442)
  hydrogen bonds       : bond        0.05624 (  231)
  hydrogen bonds       : angle       5.99023 (  672)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 MET cc_start: 0.4221 (ttp) cc_final: 0.3870 (tmm)
REVERT: B   99 TYR cc_start: 0.5685 (m-80) cc_final: 0.5344 (m-80)
REVERT: B  102 VAL cc_start: 0.7184 (t) cc_final: 0.6873 (t)
  outliers start: 4
  outliers final: 4
  residues processed: 101
  average time/residue: 0.1472
  time to fit residues: 18.7611
Evaluate side-chains
  101 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  335 TYR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  471 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 46 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4379 r_free = 0.4379 target = 0.188456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.137457 restraints weight = 16835.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.143767 restraints weight = 6724.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.147594 restraints weight = 4059.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.149877 restraints weight = 3098.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.151101 restraints weight = 2683.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.2693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4022  Z= 0.147
  Angle     :  0.514   5.358   5442  Z= 0.280
  Chirality :  0.038   0.136    612
  Planarity :  0.005   0.074    682
  Dihedral  :  5.221  51.592    554
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 13.67 %
    Favored  : 83.69 %
  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:  0.10 (0.38), residues: 500
  helix:  0.40 (0.30), residues: 301
  sheet: -0.70 (0.71), residues: 46
  loop : -0.05 (0.53), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 371 
 TYR   0.014   0.001   TYR A 125 
 PHE   0.013   0.001   PHE A 224 
 TRP   0.008   0.001   TRP A 324 
 HIS   0.004   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4022)
  covalent geometry    : angle       0.51439 ( 5442)
  hydrogen bonds       : bond        0.04586 (  231)
  hydrogen bonds       : angle       5.55379 (  672)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 MET cc_start: 0.4184 (ttp) cc_final: 0.3852 (tmm)
REVERT: A  270 MET cc_start: 0.7948 (mmt) cc_final: 0.7544 (mmp)
REVERT: B   99 TYR cc_start: 0.5670 (m-80) cc_final: 0.5357 (m-80)
  outliers start: 11
  outliers final: 8
  residues processed: 102
  average time/residue: 0.1529
  time to fit residues: 19.7998
Evaluate side-chains
  102 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  335 TYR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  471 ASN
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  104 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 28 optimal weight:    0.4980
   chunk 30 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 264 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.188058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.136914 restraints weight = 16917.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.143226 restraints weight = 6709.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.147056 restraints weight = 4043.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.149098 restraints weight = 3088.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.150251 restraints weight = 2695.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4022  Z= 0.133
  Angle     :  0.497   5.308   5442  Z= 0.269
  Chirality :  0.037   0.143    612
  Planarity :  0.004   0.056    682
  Dihedral  :  5.173  51.271    554
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 14.15 %
    Favored  : 82.49 %
  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:  0.24 (0.38), residues: 500
  helix:  0.58 (0.31), residues: 300
  sheet: -0.81 (0.71), residues: 46
  loop : -0.08 (0.54), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 371 
 TYR   0.014   0.001   TYR A 125 
 PHE   0.011   0.001   PHE A 224 
 TRP   0.007   0.001   TRP A 324 
 HIS   0.002   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4022)
  covalent geometry    : angle       0.49737 ( 5442)
  hydrogen bonds       : bond        0.04103 (  231)
  hydrogen bonds       : angle       5.23848 (  672)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 MET cc_start: 0.4186 (ttp) cc_final: 0.3838 (tmm)
REVERT: A  264 GLN cc_start: 0.7918 (tp40) cc_final: 0.7700 (tp40)
REVERT: A  270 MET cc_start: 0.7904 (mmt) cc_final: 0.7535 (mmp)
REVERT: B   49 ARG cc_start: 0.5153 (ttp-170) cc_final: 0.4888 (tpt170)
  outliers start: 14
  outliers final: 11
  residues processed: 105
  average time/residue: 0.1414
  time to fit residues: 18.7623
Evaluate side-chains
  106 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  335 TYR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  471 ASN
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  104 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 46 optimal weight:    8.9990
   chunk 40 optimal weight:    9.9990
   chunk 22 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0970
   chunk 0 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B   7 GLN ** 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 = 0.4372 r_free = 0.4372 target = 0.189207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.134171 restraints weight = 17498.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.140732 restraints weight = 7130.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.144689 restraints weight = 4393.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.146619 restraints weight = 3405.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.147935 restraints weight = 3010.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          0.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4022  Z= 0.130
  Angle     :  0.491   5.317   5442  Z= 0.266
  Chirality :  0.037   0.142    612
  Planarity :  0.004   0.048    682
  Dihedral  :  5.159  50.738    554
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 14.63 %
    Favored  : 81.77 %
  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:  0.30 (0.38), residues: 500
  helix:  0.66 (0.31), residues: 300
  sheet: -0.73 (0.72), residues: 44
  loop : -0.16 (0.53), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 508 
 TYR   0.014   0.001   TYR A 125 
 PHE   0.011   0.001   PHE A 224 
 TRP   0.007   0.001   TRP A 324 
 HIS   0.002   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4022)
  covalent geometry    : angle       0.49143 ( 5442)
  hydrogen bonds       : bond        0.03948 (  231)
  hydrogen bonds       : angle       5.07952 (  672)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 MET cc_start: 0.4045 (ttp) cc_final: 0.3703 (tmm)
REVERT: A  270 MET cc_start: 0.7965 (mmt) cc_final: 0.7608 (mmp)
REVERT: B   49 ARG cc_start: 0.5179 (ttp-170) cc_final: 0.4898 (tpt170)
  outliers start: 15
  outliers final: 14
  residues processed: 107
  average time/residue: 0.1287
  time to fit residues: 17.7202
Evaluate side-chains
  110 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  240 SER
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  335 TYR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  471 ASN
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  104 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 36 optimal weight:    0.1980
   chunk 39 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 49 optimal weight:    9.9990
   chunk 45 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B   7 GLN ** 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 = 0.4378 r_free = 0.4378 target = 0.188185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.136739 restraints weight = 16637.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.143015 restraints weight = 6650.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.146835 restraints weight = 4026.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.148880 restraints weight = 3087.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.149814 restraints weight = 2696.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.3246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4022  Z= 0.126
  Angle     :  0.491   5.286   5442  Z= 0.265
  Chirality :  0.037   0.141    612
  Planarity :  0.004   0.043    682
  Dihedral  :  5.117  49.455    554
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 14.87 %
    Favored  : 80.82 %
  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:  0.39 (0.39), residues: 500
  helix:  0.74 (0.31), residues: 300
  sheet: -0.66 (0.73), residues: 44
  loop : -0.17 (0.54), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 508 
 TYR   0.014   0.001   TYR A 125 
 PHE   0.010   0.001   PHE A 224 
 TRP   0.006   0.001   TRP A 324 
 HIS   0.004   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4022)
  covalent geometry    : angle       0.49127 ( 5442)
  hydrogen bonds       : bond        0.03806 (  231)
  hydrogen bonds       : angle       4.94931 (  672)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 MET cc_start: 0.4164 (ttp) cc_final: 0.3803 (tmm)
REVERT: A  270 MET cc_start: 0.7917 (mmt) cc_final: 0.7591 (mmp)
REVERT: B   49 ARG cc_start: 0.5137 (ttp-170) cc_final: 0.4863 (tpt170)
  outliers start: 18
  outliers final: 15
  residues processed: 108
  average time/residue: 0.1132
  time to fit residues: 15.6408
Evaluate side-chains
  113 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  240 SER
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  335 TYR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  471 ASN
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  104 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 47 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 7 optimal weight:    0.4980
   chunk 45 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 477 HIS
** B   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.187334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.135500 restraints weight = 16936.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.141804 restraints weight = 6770.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.145722 restraints weight = 4101.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.147820 restraints weight = 3130.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.148761 restraints weight = 2720.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.3371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4022  Z= 0.147
  Angle     :  0.503   5.324   5442  Z= 0.273
  Chirality :  0.038   0.140    612
  Planarity :  0.004   0.042    682
  Dihedral  :  5.147  49.172    554
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 14.39 %
    Favored  : 81.29 %
  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:  0.23 (0.38), residues: 500
  helix:  0.66 (0.31), residues: 301
  sheet: -0.63 (0.73), residues: 44
  loop : -0.39 (0.52), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 508 
 TYR   0.015   0.001   TYR A 125 
 PHE   0.012   0.001   PHE A 224 
 TRP   0.006   0.001   TRP A 324 
 HIS   0.004   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4022)
  covalent geometry    : angle       0.50344 ( 5442)
  hydrogen bonds       : bond        0.03942 (  231)
  hydrogen bonds       : angle       4.97713 (  672)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 MET cc_start: 0.4172 (ttp) cc_final: 0.3804 (tmm)
REVERT: A  270 MET cc_start: 0.7923 (mmt) cc_final: 0.7612 (mmp)
REVERT: A  477 HIS cc_start: 0.6218 (OUTLIER) cc_final: 0.5988 (t70)
REVERT: B   49 ARG cc_start: 0.5131 (ttp-170) cc_final: 0.4858 (tpt170)
  outliers start: 18
  outliers final: 16
  residues processed: 111
  average time/residue: 0.1253
  time to fit residues: 17.7879
Evaluate side-chains
  114 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  240 SER
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  335 TYR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  471 ASN
Chi-restraints excluded: chain A residue  477 HIS
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  104 GLU
Chi-restraints excluded: chain B residue  118 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 36 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** B   7 GLN ** 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 = 0.4368 r_free = 0.4368 target = 0.188944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.133821 restraints weight = 17689.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.140464 restraints weight = 7173.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.144430 restraints weight = 4402.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.146265 restraints weight = 3401.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.147584 restraints weight = 3017.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4022  Z= 0.136
  Angle     :  0.500   5.286   5442  Z= 0.272
  Chirality :  0.037   0.140    612
  Planarity :  0.004   0.040    682
  Dihedral  :  5.147  48.736    554
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 15.11 %
    Favored  : 81.06 %
  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:  0.25 (0.38), residues: 500
  helix:  0.71 (0.31), residues: 300
  sheet: -0.60 (0.73), residues: 44
  loop : -0.47 (0.52), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 508 
 TYR   0.015   0.001   TYR A 125 
 PHE   0.011   0.001   PHE A 224 
 TRP   0.006   0.001   TRP A 324 
 HIS   0.005   0.001   HIS A 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 4022)
  covalent geometry    : angle       0.49971 ( 5442)
  hydrogen bonds       : bond        0.03915 (  231)
  hydrogen bonds       : angle       4.92294 (  672)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 MET cc_start: 0.4049 (ttp) cc_final: 0.3691 (tmm)
REVERT: A  270 MET cc_start: 0.7943 (mmt) cc_final: 0.7606 (mmp)
REVERT: B   49 ARG cc_start: 0.5176 (ttp-170) cc_final: 0.4886 (tpt170)
  outliers start: 16
  outliers final: 16
  residues processed: 107
  average time/residue: 0.1116
  time to fit residues: 15.1755
Evaluate side-chains
  113 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  240 SER
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  335 TYR
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  471 ASN
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  104 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** B   7 GLN ** 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 = 0.4349 r_free = 0.4349 target = 0.185648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.132871 restraints weight = 16859.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.139125 restraints weight = 6797.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.143056 restraints weight = 4168.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.145134 restraints weight = 3199.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.146310 restraints weight = 2795.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7187
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4022  Z= 0.162
  Angle     :  0.531   5.456   5442  Z= 0.290
  Chirality :  0.038   0.139    612
  Planarity :  0.004   0.040    682
  Dihedral  :  5.198  47.823    554
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 15.59 %
    Favored  : 80.34 %
  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:  0.16 (0.38), residues: 500
  helix:  0.67 (0.30), residues: 299
  sheet: -0.58 (0.73), residues: 44
  loop : -0.57 (0.50), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 508 
 TYR   0.016   0.002   TYR A 125 
 PHE   0.014   0.001   PHE A 224 
 TRP   0.006   0.001   TRP A 324 
 HIS   0.005   0.001   HIS A 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 4022)
  covalent geometry    : angle       0.53124 ( 5442)
  hydrogen bonds       : bond        0.04098 (  231)
  hydrogen bonds       : angle       5.02359 (  672)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 MET cc_start: 0.4180 (ttp) cc_final: 0.3803 (tmm)
REVERT: A  270 MET cc_start: 0.7904 (mmt) cc_final: 0.7579 (mmp)
  outliers start: 17
  outliers final: 16
  residues processed: 108
  average time/residue: 0.1110
  time to fit residues: 15.4094
Evaluate side-chains
  112 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  240 SER
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  335 TYR
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  471 ASN
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  104 GLU
Chi-restraints excluded: chain B residue  118 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 5 optimal weight:    0.4980
   chunk 13 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B   7 GLN ** 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 = 0.4362 r_free = 0.4362 target = 0.186906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.135669 restraints weight = 16697.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.141930 restraints weight = 6634.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 69)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.145752 restraints weight = 4006.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.147741 restraints weight = 3065.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.148932 restraints weight = 2673.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
moved from start:          0.3520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4022  Z= 0.129
  Angle     :  0.498   5.301   5442  Z= 0.269
  Chirality :  0.037   0.140    612
  Planarity :  0.004   0.035    682
  Dihedral  :  5.156  48.500    554
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 15.59 %
    Favored  : 80.58 %
  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:  0.33 (0.38), residues: 500
  helix:  0.77 (0.31), residues: 299
  sheet: -0.52 (0.72), residues: 44
  loop : -0.43 (0.52), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 508 
 TYR   0.014   0.001   TYR A 125 
 PHE   0.010   0.001   PHE A 224 
 TRP   0.007   0.001   TRP A 324 
 HIS   0.003   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 4022)
  covalent geometry    : angle       0.49836 ( 5442)
  hydrogen bonds       : bond        0.03786 (  231)
  hydrogen bonds       : angle       4.83020 (  672)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 MET cc_start: 0.4230 (ttp) cc_final: 0.3841 (tmm)
REVERT: A  270 MET cc_start: 0.7912 (mmt) cc_final: 0.7614 (mmp)
  outliers start: 16
  outliers final: 16
  residues processed: 106
  average time/residue: 0.1166
  time to fit residues: 15.8880
Evaluate side-chains
  110 residues out of total 417 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  162 SER
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  240 SER
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  335 TYR
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  471 ASN
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  104 GLU
Chi-restraints excluded: chain B residue  118 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0980
   chunk 21 optimal weight:    0.8980
   chunk 15 optimal weight:    0.3980
   chunk 7 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0980
   chunk 43 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** B   7 GLN ** 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 = 0.4365 r_free = 0.4365 target = 0.188544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.134108 restraints weight = 17335.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.140617 restraints weight = 7021.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.144483 restraints weight = 4286.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.146741 restraints weight = 3309.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.147822 restraints weight = 2890.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4022  Z= 0.109
  Angle     :  0.483   5.282   5442  Z= 0.258
  Chirality :  0.037   0.142    612
  Planarity :  0.004   0.035    682
  Dihedral  :  5.079  50.034    554
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 15.83 %
    Favored  : 80.58 %
  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:  0.52 (0.39), residues: 500
  helix:  0.93 (0.31), residues: 299
  sheet: -0.50 (0.73), residues: 44
  loop : -0.33 (0.53), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 508 
 TYR   0.013   0.001   TYR A 125 
 PHE   0.007   0.001   PHE A 224 
 TRP   0.006   0.001   TRP A 324 
 HIS   0.003   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 4022)
  covalent geometry    : angle       0.48343 ( 5442)
  hydrogen bonds       : bond        0.03532 (  231)
  hydrogen bonds       : angle       4.64527 (  672)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1913.95 seconds
wall clock time: 33 minutes 11.55 seconds (1991.55 seconds total)