Starting phenix.real_space_refine
on Wed Sep 17 06:57:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y7z_39027/09_2025/8y7z_39027.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y7z_39027/09_2025/8y7z_39027.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y7z_39027/09_2025/8y7z_39027.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y7z_39027/09_2025/8y7z_39027.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y7z_39027/09_2025/8y7z_39027.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y7z_39027/09_2025/8y7z_39027.cif"
  }
  resolution = 2.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.098
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: 6
    Type Number    sf(0)   Gaussians
     P      41      5.49       5
     Mg      1      5.21       5
     S      22      5.16       5
     C    4007      2.51       5
     N    1117      2.21       5
     O    1300      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6488
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 3629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 456, 3629
          Classifications: {'peptide': 456}
          Link IDs: {'PTRANS': 27, 'TRANS': 428}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 2005
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 252, 2005
          Classifications: {'peptide': 252}
          Link IDs: {'PTRANS': 9, 'TRANS': 242}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 442
          Classifications: {'RNA': 21}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10}
          Link IDs: {'rna2p': 2, 'rna3p': 18}
    Chain: "D"
      Number of atoms: 411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 411
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.84, per 1000 atoms: 0.28
  Number of scatterers: 6488
  At special positions: 0
  Unit cell: (68.641, 79.392, 106.683, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      22     16.00
     P      41     15.00
     Mg      1     11.99
     O    1300      8.00
     N    1117      7.00
     C    4007      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 304.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1326

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 11 sheets defined
      37.6% alpha, 24.3% beta
      15 base pairs and 30 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'B' and resid 29 through 38
    Processing helix  chain 'B' and resid 39 through 43
      removed outlier: 3.847A  pdb=" N   CYS B  43 " --> pdb=" O   TYR B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 73
      removed outlier: 3.618A  pdb=" N   LEU B  64 " --> pdb=" O   HIS B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 95
    Processing helix  chain 'B' and resid 102 through 104
      No H-bonds generated for 'chain 'B' and resid 102 through 104'
    Processing helix  chain 'B' and resid 110 through 119
      removed outlier: 3.826A  pdb=" N   HIS B 114 " --> pdb=" O   LEU B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 132
    Processing helix  chain 'B' and resid 133 through 139
      removed outlier: 3.788A  pdb=" N   ARG B 138 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 157
      removed outlier: 4.769A  pdb=" N   LYS B 156 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 173
    Processing helix  chain 'B' and resid 184 through 190
      removed outlier: 3.966A  pdb=" N   LEU B 188 " --> pdb=" O   ASN B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 208
      removed outlier: 3.834A  pdb=" N   VAL B 196 " --> pdb=" O   CYS B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 294
      removed outlier: 3.550A  pdb=" N   SER B 282 " --> pdb=" O   GLN B 278 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   SER B 294 " --> pdb=" O   LEU B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 323
      removed outlier: 3.719A  pdb=" N   PHE B 323 " --> pdb=" O   ALA B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 417 through 428
      removed outlier: 4.717A  pdb=" N   THR B 421 " --> pdb=" O   GLY B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 459
    Processing helix  chain 'B' and resid 470 through 472
      No H-bonds generated for 'chain 'B' and resid 470 through 472'
    Processing helix  chain 'A' and resid 355 through 367
    Processing helix  chain 'A' and resid 383 through 391
      removed outlier: 3.555A  pdb=" N   ILE A 387 " --> pdb=" O   GLY A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 414
    Processing helix  chain 'A' and resid 414 through 430
    Processing helix  chain 'A' and resid 455 through 457
      No H-bonds generated for 'chain 'A' and resid 455 through 457'
    Processing helix  chain 'A' and resid 458 through 466
    Processing helix  chain 'A' and resid 513 through 519
      removed outlier: 4.878A  pdb=" N   GLU A 518 " --> pdb=" O   ASP A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 529
    Processing helix  chain 'A' and resid 532 through 549
    Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 13
      removed outlier: 6.401A  pdb=" N   ILE B 303 " --> pdb=" O   GLU B 330 " (cutoff:3.500A)
      removed outlier: 7.335A  pdb=" N   VAL B 332 " --> pdb=" O   ILE B 303 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ILE B 305 " --> pdb=" O   VAL B 332 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   ILE B 334 " --> pdb=" O   ILE B 305 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   LYS B 307 " --> pdb=" O   ILE B 334 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ALA B 223 " --> pdb=" O   PHE B 304 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   HIS B 306 " --> pdb=" O   ALA B 223 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ILE B 225 " --> pdb=" O   HIS B 306 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 27
      removed outlier: 3.533A  pdb=" N   ARG B  25 " --> pdb=" O   PHE B  21 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99
      removed outlier: 8.493A  pdb=" N   CYS B 107 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   TYR B  54 " --> pdb=" O   CYS B 107 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 99
      removed outlier: 6.407A  pdb=" N   ARG B  51 " --> pdb=" O   VAL B 145 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   LEU B 147 " --> pdb=" O   ARG B  51 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   ALA B  53 " --> pdb=" O   LEU B 147 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   TYR B 149 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   LEU B  55 " --> pdb=" O   TYR B 149 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   LEU B 146 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   ILE B 183 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   VAL B 148 " --> pdb=" O   ILE B 183 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 160
      removed outlier: 3.544A  pdb=" N   TYR B 160 " --> pdb=" O   PHE B 163 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 343 through 344
    Processing sheet with id=AA7, first strand: chain 'B' and resid 381 through 382
    Processing sheet with id=AA8, first strand: chain 'A' and resid 335 through 337
      removed outlier: 4.017A  pdb=" N   HIS A 444 " --> pdb=" O   ILE A 492 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 335 through 337
    Processing sheet with id=AB1, first strand: chain 'A' and resid 370 through 373
      removed outlier: 7.031A  pdb=" N   GLY A 382 " --> pdb=" O   ARG A 344 " (cutoff:3.500A)
      removed outlier: 10.649A  pdb=" N   ARG A 344 " --> pdb=" O   GLY A 382 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   ILE A 343 " --> pdb=" O   TYR A 403 " (cutoff:3.500A)
      removed outlier: 4.971A  pdb=" N   TYR A 403 " --> pdb=" O   ILE A 343 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   CYS A 345 " --> pdb=" O   GLN A 401 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   GLN A 401 " --> pdb=" O   CYS A 345 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   VAL A 347 " --> pdb=" O   ILE A 399 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ILE A 399 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   THR A 349 " --> pdb=" O   ASN A 397 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 558 through 561
      removed outlier: 3.560A  pdb=" N   ALA A 569 " --> pdb=" O   CYS A 561 " (cutoff:3.500A)

    250 hydrogen bonds defined for protein.
    684 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      35 hydrogen bonds
      62 hydrogen bond angles
      0 basepair planarities
      15 basepair parallelities
      30 stacking parallelities
  Total time for adding SS restraints: 1.33

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1866
        1.34 -     1.45: 1407
        1.45 -     1.57: 3336
        1.57 -     1.69: 81
        1.69 -     1.81: 32
  Bond restraints: 6722
  Sorted by residual:
  bond pdb=" CA  ASN B 121 "
       pdb=" CB  ASN B 121 "
    ideal  model  delta    sigma   weight residual
    1.531  1.579 -0.049 3.28e-02 9.30e+02 2.21e+00
  bond pdb=" C3'  DA D  18 "
       pdb=" O3'  DA D  18 "
    ideal  model  delta    sigma   weight residual
    1.422  1.459 -0.037 3.00e-02 1.11e+03 1.52e+00
  bond pdb=" C3'  DT D  23 "
       pdb=" O3'  DT D  23 "
    ideal  model  delta    sigma   weight residual
    1.422  1.458 -0.036 3.00e-02 1.11e+03 1.41e+00
  bond pdb=" CB  ASN B 296 "
       pdb=" CG  ASN B 296 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.06e+00
  bond pdb=" CG  LEU B 288 "
       pdb=" CD2 LEU B 288 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.55e-01
  ... (remaining 6717 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 9046
        1.78 -     3.55: 215
        3.55 -     5.33: 24
        5.33 -     7.11: 6
        7.11 -     8.88: 2
  Bond angle restraints: 9293
  Sorted by residual:
  angle pdb=" CB  MET B 383 "
        pdb=" CG  MET B 383 "
        pdb=" SD  MET B 383 "
      ideal   model   delta    sigma   weight residual
     112.70  121.58   -8.88 3.00e+00 1.11e-01 8.77e+00
  angle pdb=" O4'  DT D  12 "
        pdb=" C1'  DT D  12 "
        pdb=" N1   DT D  12 "
      ideal   model   delta    sigma   weight residual
     108.40  112.58   -4.18 1.50e+00 4.44e-01 7.77e+00
  angle pdb=" C   HIS A 441 "
        pdb=" CA  HIS A 441 "
        pdb=" CB  HIS A 441 "
      ideal   model   delta    sigma   weight residual
     110.42  115.96   -5.54 1.99e+00 2.53e-01 7.75e+00
  angle pdb=" N   GLY B 209 "
        pdb=" CA  GLY B 209 "
        pdb=" C   GLY B 209 "
      ideal   model   delta    sigma   weight residual
     113.18  107.21    5.97 2.37e+00 1.78e-01 6.34e+00
  angle pdb=" N   HIS A 441 "
        pdb=" CA  HIS A 441 "
        pdb=" C   HIS A 441 "
      ideal   model   delta    sigma   weight residual
     110.80  105.57    5.23 2.13e+00 2.20e-01 6.02e+00
  ... (remaining 9288 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.78: 3680
       32.78 -    65.56: 299
       65.56 -    98.34: 20
       98.34 -   131.13: 0
      131.13 -   163.91: 2
  Dihedral angle restraints: 4001
    sinusoidal: 1942
      harmonic: 2059
  Sorted by residual:
  dihedral pdb=" CA  LEU B  46 "
           pdb=" C   LEU B  46 "
           pdb=" N   PRO B  47 "
           pdb=" CA  PRO B  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.12   22.88     0      5.00e+00 4.00e-02 2.09e+01
  dihedral pdb=" C4'  DT D  23 "
           pdb=" C3'  DT D  23 "
           pdb=" O3'  DT D  23 "
           pdb=" P    DA D  24 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   56.09  163.91     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'  DA D  18 "
           pdb=" C3'  DA D  18 "
           pdb=" O3'  DA D  18 "
           pdb=" P    DG D  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   65.62  154.38     1      3.50e+01 8.16e-04 1.49e+01
  ... (remaining 3998 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 756
       0.040 -    0.080: 205
       0.080 -    0.120: 70
       0.120 -    0.160: 14
       0.160 -    0.200: 2
  Chirality restraints: 1047
  Sorted by residual:
  chirality pdb=" CB  VAL B 247 "
            pdb=" CA  VAL B 247 "
            pdb=" CG1 VAL B 247 "
            pdb=" CG2 VAL B 247 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" C1'   A C  20 "
            pdb=" O4'   A C  20 "
            pdb=" C2'   A C  20 "
            pdb=" N9    A C  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.28    0.18 2.00e-01 2.50e+01 7.77e-01
  chirality pdb=" CB  ILE B 225 "
            pdb=" CA  ILE B 225 "
            pdb=" CG1 ILE B 225 "
            pdb=" CG2 ILE B 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.85e-01
  ... (remaining 1044 not shown)

  Planarity restraints: 1043
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT D  12 "   -0.027 2.00e-02 2.50e+03   1.44e-02 5.21e+00
        pdb=" N1   DT D  12 "    0.036 2.00e-02 2.50e+03
        pdb=" C2   DT D  12 "    0.002 2.00e-02 2.50e+03
        pdb=" O2   DT D  12 "    0.000 2.00e-02 2.50e+03
        pdb=" N3   DT D  12 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DT D  12 "   -0.004 2.00e-02 2.50e+03
        pdb=" O4   DT D  12 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5   DT D  12 "   -0.001 2.00e-02 2.50e+03
        pdb=" C7   DT D  12 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DT D  12 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C C   5 "    0.026 2.00e-02 2.50e+03   1.38e-02 4.31e+00
        pdb=" N1    C C   5 "   -0.030 2.00e-02 2.50e+03
        pdb=" C2    C C   5 "    0.000 2.00e-02 2.50e+03
        pdb=" O2    C C   5 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3    C C   5 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    C C   5 "    0.003 2.00e-02 2.50e+03
        pdb=" N4    C C   5 "    0.007 2.00e-02 2.50e+03
        pdb=" C5    C C   5 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    C C   5 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C C   4 "   -0.027 2.00e-02 2.50e+03   1.35e-02 4.11e+00
        pdb=" N1    C C   4 "    0.027 2.00e-02 2.50e+03
        pdb=" C2    C C   4 "    0.005 2.00e-02 2.50e+03
        pdb=" O2    C C   4 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    C C   4 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    C C   4 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4    C C   4 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5    C C   4 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    C C   4 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1040 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 57
        2.55 -     3.13: 4821
        3.13 -     3.72: 11324
        3.72 -     4.31: 16395
        4.31 -     4.90: 25575
  Nonbonded interactions: 58172
  Sorted by model distance:
  nonbonded pdb=" OP1   A C   1 "
            pdb="MG    MG B 501 "
     model   vdw
     1.958 2.170
  nonbonded pdb=" ND2 ASN B 434 "
            pdb="MG    MG B 501 "
     model   vdw
     2.059 2.250
  nonbonded pdb=" N2    G C  11 "
            pdb=" O2   DC D  13 "
     model   vdw
     2.138 2.496
  nonbonded pdb=" O   THR B 242 "
            pdb=" OG1 THR B 262 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" N2    G C  16 "
            pdb=" O2   DC D   8 "
     model   vdw
     2.147 2.496
  ... (remaining 58167 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 individual isotropic
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:             3.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     8.620
  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:6.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
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      :  0.004   0.049   6722  Z= 0.168
  Angle     :  0.657   8.885   9293  Z= 0.352
  Chirality :  0.043   0.200   1047
  Planarity :  0.004   0.042   1043
  Dihedral  : 20.761 163.906   2675
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 28.62 %
    Favored  : 71.05 %
  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: -0.35 (0.32), residues: 698
  helix:  0.40 (0.35), residues: 217
  sheet: -0.45 (0.38), residues: 166
  loop : -0.41 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 138 
 TYR   0.021   0.002   TYR B  84 
 PHE   0.012   0.002   PHE B 257 
 TRP   0.007   0.001   TRP B 198 
 HIS   0.003   0.001   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 6722)
  covalent geometry    : angle       0.65739 ( 9293)
  hydrogen bonds       : bond        0.08523 (  269)
  hydrogen bonds       : angle       5.44428 (  746)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 0.207 
Fit side-chains
REVERT: B  299 MET cc_start: 0.7363 (mmt) cc_final: 0.6900 (mmm)
REVERT: A  508 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6826 (mm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 85
  average time/residue: 0.6053
  time to fit residues: 53.9599
Evaluate side-chains
  75 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  247 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0570
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 GLN
A 437 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.171114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.141577 restraints weight = 5827.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 1.45
r_work: 0.3621 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3514 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.0667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6722  Z= 0.166
  Angle     :  0.616   8.457   9293  Z= 0.324
  Chirality :  0.042   0.170   1047
  Planarity :  0.005   0.040   1043
  Dihedral  : 19.453 164.168   1326
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 26.81 %
    Favored  : 68.91 %
  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 (0.32), residues: 698
  helix:  0.45 (0.34), residues: 217
  sheet: -0.46 (0.39), residues: 165
  loop : -0.27 (0.37), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 138 
 TYR   0.018   0.002   TYR B  84 
 PHE   0.015   0.002   PHE B 255 
 TRP   0.006   0.001   TRP B 198 
 HIS   0.004   0.001   HIS B  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 6722)
  covalent geometry    : angle       0.61596 ( 9293)
  hydrogen bonds       : bond        0.05430 (  269)
  hydrogen bonds       : angle       5.24117 (  746)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 82
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: B  315 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7335 (mt-10)
REVERT: B  383 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7645 (mmm)
REVERT: A  366 LYS cc_start: 0.7612 (mmmm) cc_final: 0.7392 (mmtm)
REVERT: A  484 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8061 (tp)
REVERT: A  508 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7182 (mm-30)
  outliers start: 26
  outliers final: 11
  residues processed: 100
  average time/residue: 0.6161
  time to fit residues: 64.5456
Evaluate side-chains
  87 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 GLU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  383 MET
Chi-restraints excluded: chain B residue  392 GLN
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  484 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 59 optimal weight:    0.4980
   chunk 65 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 281 GLN
A 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.163330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.133295 restraints weight = 5809.907|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 1.45
r_work: 0.3527 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3418 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.1141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.047   6722  Z= 0.341
  Angle     :  0.768   8.023   9293  Z= 0.400
  Chirality :  0.049   0.211   1047
  Planarity :  0.006   0.051   1043
  Dihedral  : 19.490 166.148   1326
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 25.49 %
    Favored  : 67.76 %
  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: -0.68 (0.31), residues: 698
  helix: -0.14 (0.32), residues: 217
  sheet: -0.62 (0.39), residues: 165
  loop : -0.40 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 138 
 TYR   0.023   0.003   TYR B  84 
 PHE   0.018   0.003   PHE A 523 
 TRP   0.011   0.002   TRP A 510 
 HIS   0.006   0.001   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00770 ( 6722)
  covalent geometry    : angle       0.76814 ( 9293)
  hydrogen bonds       : bond        0.06447 (  269)
  hydrogen bonds       : angle       5.62093 (  746)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 78
  time to evaluate  : 0.248 
Fit side-chains
REVERT: B  110 LEU cc_start: 0.7700 (mp) cc_final: 0.7478 (mp)
REVERT: B  222 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6759 (mm-30)
REVERT: B  315 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7410 (mt-10)
REVERT: B  330 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7036 (tp30)
REVERT: A  484 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8088 (tp)
  outliers start: 41
  outliers final: 17
  residues processed: 106
  average time/residue: 0.5927
  time to fit residues: 65.9991
Evaluate side-chains
  92 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain B residue  239 GLU
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  330 GLU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  392 GLN
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  514 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0770
   chunk 8 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  49 GLN
A 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.170074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.140830 restraints weight = 5792.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 1.42
r_work: 0.3609 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3502 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.0986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6722  Z= 0.160
  Angle     :  0.614   7.989   9293  Z= 0.323
  Chirality :  0.042   0.158   1047
  Planarity :  0.005   0.040   1043
  Dihedral  : 19.339 164.447   1326
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 27.63 %
    Favored  : 67.60 %
  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: -0.42 (0.32), residues: 698
  helix:  0.36 (0.34), residues: 218
  sheet: -0.68 (0.39), residues: 166
  loop : -0.35 (0.37), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 138 
 TYR   0.021   0.002   TYR B  84 
 PHE   0.019   0.002   PHE B 255 
 TRP   0.007   0.001   TRP B 198 
 HIS   0.004   0.001   HIS B  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 6722)
  covalent geometry    : angle       0.61417 ( 9293)
  hydrogen bonds       : bond        0.05381 (  269)
  hydrogen bonds       : angle       5.28562 (  746)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  484 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8111 (tp)
  outliers start: 29
  outliers final: 15
  residues processed: 101
  average time/residue: 0.5959
  time to fit residues: 63.2285
Evaluate side-chains
  91 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  514 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 20 optimal weight:    0.2980
   chunk 28 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 23 optimal weight:    0.3980
   chunk 11 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 68 optimal weight:    0.3980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  49 GLN
B 281 GLN
A 409 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.167809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.138363 restraints weight = 5868.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 1.43
r_work: 0.3582 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.1039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6722  Z= 0.192
  Angle     :  0.636   8.335   9293  Z= 0.333
  Chirality :  0.043   0.156   1047
  Planarity :  0.005   0.045   1043
  Dihedral  : 19.308 164.881   1326
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 27.63 %
    Favored  : 67.76 %
  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: -0.35 (0.32), residues: 698
  helix:  0.39 (0.34), residues: 218
  sheet: -0.62 (0.39), residues: 165
  loop : -0.29 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 138 
 TYR   0.023   0.002   TYR B  84 
 PHE   0.017   0.002   PHE B 255 
 TRP   0.007   0.001   TRP B 198 
 HIS   0.004   0.001   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 6722)
  covalent geometry    : angle       0.63591 ( 9293)
  hydrogen bonds       : bond        0.05469 (  269)
  hydrogen bonds       : angle       5.27708 (  746)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 78
  time to evaluate  : 0.234 
Fit side-chains
REVERT: B  330 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6971 (tp30)
REVERT: A  484 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8107 (tp)
  outliers start: 28
  outliers final: 18
  residues processed: 98
  average time/residue: 0.6016
  time to fit residues: 61.8622
Evaluate side-chains
  93 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  239 GLU
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  330 GLU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  461 GLU
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  484 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  49 GLN
A 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.167990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.138421 restraints weight = 5852.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 1.43
r_work: 0.3585 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3477 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.1110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6722  Z= 0.193
  Angle     :  0.634   7.934   9293  Z= 0.331
  Chirality :  0.043   0.156   1047
  Planarity :  0.005   0.046   1043
  Dihedral  : 19.288 164.819   1326
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 26.81 %
    Favored  : 67.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.32), residues: 698
  helix:  0.36 (0.34), residues: 218
  sheet: -0.63 (0.39), residues: 165
  loop : -0.31 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 138 
 TYR   0.023   0.002   TYR B  84 
 PHE   0.016   0.002   PHE B 255 
 TRP   0.007   0.001   TRP B 198 
 HIS   0.004   0.001   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 6722)
  covalent geometry    : angle       0.63407 ( 9293)
  hydrogen bonds       : bond        0.05437 (  269)
  hydrogen bonds       : angle       5.27449 (  746)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 79
  time to evaluate  : 0.185 
Fit side-chains
REVERT: B  110 LEU cc_start: 0.7692 (mp) cc_final: 0.7478 (mp)
REVERT: B  298 ARG cc_start: 0.6733 (ttp-110) cc_final: 0.6293 (ttp-170)
REVERT: B  330 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6981 (tp30)
REVERT: B  457 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7812 (ttmt)
REVERT: A  484 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8098 (tp)
  outliers start: 36
  outliers final: 19
  residues processed: 108
  average time/residue: 0.5642
  time to fit residues: 64.0482
Evaluate side-chains
  97 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 75
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  330 GLU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  457 LYS
Chi-restraints excluded: chain B residue  461 GLU
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  514 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0980
   chunk 61 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 62 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B   7 GLN
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  49 GLN
A 409 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.169883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.140709 restraints weight = 5834.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 1.43
r_work: 0.3611 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3503 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.1127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6722  Z= 0.164
  Angle     :  0.612   8.056   9293  Z= 0.320
  Chirality :  0.042   0.168   1047
  Planarity :  0.005   0.050   1043
  Dihedral  : 19.253 164.662   1326
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 27.47 %
    Favored  : 67.43 %
  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: -0.28 (0.32), residues: 698
  helix:  0.52 (0.34), residues: 217
  sheet: -0.62 (0.39), residues: 165
  loop : -0.29 (0.37), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 138 
 TYR   0.022   0.002   TYR B  84 
 PHE   0.014   0.002   PHE B 255 
 TRP   0.006   0.001   TRP B 198 
 HIS   0.003   0.001   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 6722)
  covalent geometry    : angle       0.61232 ( 9293)
  hydrogen bonds       : bond        0.05337 (  269)
  hydrogen bonds       : angle       5.16698 (  746)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 80
  time to evaluate  : 0.239 
Fit side-chains
REVERT: B  315 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7192 (mt-10)
REVERT: B  330 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6956 (tp30)
REVERT: B  457 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7791 (ttmt)
REVERT: A  484 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8053 (tp)
REVERT: A  508 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7220 (mm-30)
REVERT: A  512 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6470 (tmtp)
  outliers start: 31
  outliers final: 20
  residues processed: 104
  average time/residue: 0.6001
  time to fit residues: 65.5281
Evaluate side-chains
  100 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 76
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  330 GLU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  457 LYS
Chi-restraints excluded: chain B residue  461 GLU
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  512 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0870
   chunk 39 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  49 GLN
A 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.170331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.141106 restraints weight = 5822.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 1.44
r_work: 0.3614 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3507 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.1199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6722  Z= 0.161
  Angle     :  0.611   9.182   9293  Z= 0.318
  Chirality :  0.041   0.154   1047
  Planarity :  0.005   0.054   1043
  Dihedral  : 19.257 164.755   1326
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 27.30 %
    Favored  : 67.60 %
  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: -0.29 (0.32), residues: 698
  helix:  0.53 (0.34), residues: 218
  sheet: -0.60 (0.39), residues: 165
  loop : -0.32 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B 138 
 TYR   0.022   0.002   TYR B  84 
 PHE   0.015   0.002   PHE B 255 
 TRP   0.006   0.001   TRP B 198 
 HIS   0.003   0.001   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 6722)
  covalent geometry    : angle       0.61097 ( 9293)
  hydrogen bonds       : bond        0.05320 (  269)
  hydrogen bonds       : angle       5.12242 (  746)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 79
  time to evaluate  : 0.233 
Fit side-chains
REVERT: B  315 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7178 (mt-10)
REVERT: B  330 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6950 (tp30)
REVERT: B  457 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7801 (ttmt)
REVERT: A  362 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6419 (mtm-85)
REVERT: A  484 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8038 (tp)
REVERT: A  508 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7159 (mm-30)
REVERT: A  512 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6467 (tmtp)
  outliers start: 31
  outliers final: 21
  residues processed: 103
  average time/residue: 0.6051
  time to fit residues: 65.3769
Evaluate side-chains
  103 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 77
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  330 GLU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  457 LYS
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain A residue  362 ARG
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain A residue  514 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  49 GLN
B 281 GLN
A 409 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.164549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.134347 restraints weight = 5888.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 1.47
r_work: 0.3537 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3428 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.1336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044   6722  Z= 0.306
  Angle     :  0.746   8.025   9293  Z= 0.386
  Chirality :  0.047   0.188   1047
  Planarity :  0.006   0.053   1043
  Dihedral  : 19.360 166.175   1326
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 26.97 %
    Favored  : 67.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.64 (0.31), residues: 698
  helix:  0.05 (0.33), residues: 217
  sheet: -0.72 (0.39), residues: 165
  loop : -0.43 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 138 
 TYR   0.029   0.002   TYR B  84 
 PHE   0.018   0.003   PHE B 257 
 TRP   0.010   0.002   TRP A 510 
 HIS   0.006   0.001   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00691 ( 6722)
  covalent geometry    : angle       0.74599 ( 9293)
  hydrogen bonds       : bond        0.06121 (  269)
  hydrogen bonds       : angle       5.46142 (  746)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 76
  time to evaluate  : 0.226 
Fit side-chains
REVERT: B  110 LEU cc_start: 0.7740 (mp) cc_final: 0.7521 (mp)
REVERT: B  222 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6504 (mm-30)
REVERT: B  315 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7140 (mt-10)
REVERT: B  330 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7079 (tp30)
REVERT: B  457 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7875 (ttmt)
REVERT: A  484 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8112 (tp)
  outliers start: 35
  outliers final: 21
  residues processed: 102
  average time/residue: 0.5913
  time to fit residues: 63.3554
Evaluate side-chains
  99 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  330 GLU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  392 GLN
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  457 LYS
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  435 ILE
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  514 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  49 GLN
B 281 GLN
A 409 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.168951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.139469 restraints weight = 5797.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3700 rms_B_bonded: 1.43
r_work: 0.3595 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3488 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6722  Z= 0.181
  Angle     :  0.644   8.719   9293  Z= 0.335
  Chirality :  0.042   0.155   1047
  Planarity :  0.005   0.056   1043
  Dihedral  : 19.286 164.861   1326
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 28.62 %
    Favored  : 66.94 %
  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: -0.42 (0.32), residues: 698
  helix:  0.40 (0.34), residues: 217
  sheet: -0.69 (0.40), residues: 165
  loop : -0.37 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 298 
 TYR   0.025   0.002   TYR B  84 
 PHE   0.016   0.002   PHE B 257 
 TRP   0.005   0.001   TRP B 377 
 HIS   0.003   0.001   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 6722)
  covalent geometry    : angle       0.64352 ( 9293)
  hydrogen bonds       : bond        0.05398 (  269)
  hydrogen bonds       : angle       5.27022 (  746)

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

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

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1396 Ramachandran restraints generated.
    698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 74
  time to evaluate  : 0.234 
Fit side-chains
REVERT: B  315 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7139 (mt-10)
REVERT: B  330 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6991 (tp30)
REVERT: B  457 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7829 (ttmt)
REVERT: A  484 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8105 (tp)
  outliers start: 27
  outliers final: 19
  residues processed: 94
  average time/residue: 0.6075
  time to fit residues: 59.9184
Evaluate side-chains
  94 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  330 GLU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  343 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  421 THR
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  457 LYS
Chi-restraints excluded: chain B residue  466 ILE
Chi-restraints excluded: chain A residue  331 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  417 LEU
Chi-restraints excluded: chain A residue  484 LEU
Chi-restraints excluded: chain A residue  514 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 37 optimal weight:    0.0770
   chunk 15 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 67 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
** B  29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  49 GLN
B 281 GLN
A 409 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.171817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.142679 restraints weight = 5828.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 1.43
r_work: 0.3631 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3524 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6722  Z= 0.151
  Angle     :  0.612   8.997   9293  Z= 0.318
  Chirality :  0.041   0.153   1047
  Planarity :  0.005   0.058   1043
  Dihedral  : 19.249 164.689   1326
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 28.95 %
    Favored  : 67.11 %
  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: -0.27 (0.32), residues: 698
  helix:  0.64 (0.35), residues: 216
  sheet: -0.65 (0.38), residues: 175
  loop : -0.33 (0.37), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 298 
 TYR   0.023   0.002   TYR B  84 
 PHE   0.016   0.002   PHE B 255 
 TRP   0.006   0.001   TRP B 198 
 HIS   0.003   0.001   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6722)
  covalent geometry    : angle       0.61179 ( 9293)
  hydrogen bonds       : bond        0.05290 (  269)
  hydrogen bonds       : angle       5.10353 (  746)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2705.26 seconds
wall clock time: 47 minutes 1.88 seconds (2821.88 seconds total)