Starting phenix.real_space_refine
on Fri Aug 22 18:21:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ga5_29890/08_2025/8ga5_29890.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ga5_29890/08_2025/8ga5_29890.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ga5_29890/08_2025/8ga5_29890.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ga5_29890/08_2025/8ga5_29890.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ga5_29890/08_2025/8ga5_29890.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ga5_29890/08_2025/8ga5_29890.cif"
  }
  resolution = 2.6
  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=   0.002 sd=   0.091
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      42      5.16       5
     Cl      6      4.86       5
     C    4432      2.51       5
     N    1140      2.21       5
     O    1169      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  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: 6789
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3377
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 450, 3377
          Classifications: {'peptide': 450}
          Link IDs: {'PTRANS': 19, 'TRANS': 430}
    Chain: "B"
      Number of atoms: 3377
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 450, 3377
          Classifications: {'peptide': 450}
          Link IDs: {'PTRANS': 19, 'TRANS': 430}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CL': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CL': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 17
          Classifications: {'water': 17}
          Link IDs: {None: 16}
    Chain: "B"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
  Time building chain proxies: 2.04, per 1000 atoms: 0.30
  Number of scatterers: 6789
  At special positions: 0
  Unit cell: (75.9, 71.775, 112.2, 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)
     Cl      6     17.00
     S      42     16.00
     O    1169      8.00
     N    1140      7.00
     C    4432      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  25 " - pdb=" SG  CYS B 450 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 450 " - pdb=" SG  CYS B  25 " distance=2.02

  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: 0.58
  Conformation dependent library (CDL) restraints added in 466.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1572

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 0 sheets defined
      81.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 26
      removed outlier: 3.635A  pdb=" N   CYS A  25 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU A  26 " --> pdb=" O   ILE A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 71
      removed outlier: 3.964A  pdb=" N   LEU A  36 " --> pdb=" O   PRO A  32 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   HIS A  70 " --> pdb=" O   GLY A  66 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   THR A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 100
      removed outlier: 3.594A  pdb=" N   ALA A  85 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   SER A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU A  89 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLY A  93 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 105
    Processing helix  chain 'A' and resid 108 through 116
    Processing helix  chain 'A' and resid 126 through 141
    Processing helix  chain 'A' and resid 147 through 166
    Processing helix  chain 'A' and resid 170 through 190
      removed outlier: 3.584A  pdb=" N   ARG A 174 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 202
      removed outlier: 3.571A  pdb=" N   ILE A 197 " --> pdb=" O   PRO A 193 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ILE A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 233
      removed outlier: 4.121A  pdb=" N   PHE A 232 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 250
      No H-bonds generated for 'chain 'A' and resid 248 through 250'
    Processing helix  chain 'A' and resid 251 through 285
      removed outlier: 4.000A  pdb=" N   TYR A 255 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      Proline residue:  A 267  - end of helix
      removed outlier: 3.966A  pdb=" N   VAL A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   HIS A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 305
      removed outlier: 3.826A  pdb=" N   LEU A 293 " --> pdb=" O   THR A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 313
      removed outlier: 3.571A  pdb=" N   SER A 313 " --> pdb=" O   PRO A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 325
      removed outlier: 3.576A  pdb=" N   ALA A 325 " --> pdb=" O   PRO A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 349
    Processing helix  chain 'A' and resid 356 through 379
    Processing helix  chain 'A' and resid 386 through 401
      removed outlier: 3.520A  pdb=" N   ALA A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA A 392 " --> pdb=" O   THR A 388 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLY A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU A 397 " --> pdb=" O   GLY A 393 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   LEU A 398 " --> pdb=" O   MET A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 417
      removed outlier: 3.519A  pdb=" N   LEU A 411 " --> pdb=" O   THR A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 420
      No H-bonds generated for 'chain 'A' and resid 418 through 420'
    Processing helix  chain 'A' and resid 421 through 439
    Processing helix  chain 'A' and resid 443 through 457
    Processing helix  chain 'B' and resid 14 through 24
    Processing helix  chain 'B' and resid 33 through 71
      removed outlier: 3.531A  pdb=" N   VAL B  51 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU B  68 " --> pdb=" O   ARG B  64 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   HIS B  70 " --> pdb=" O   GLY B  66 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   THR B  71 " --> pdb=" O   ALA B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 101
      removed outlier: 3.813A  pdb=" N   SER B  86 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL B  97 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 105
    Processing helix  chain 'B' and resid 108 through 117
    Processing helix  chain 'B' and resid 123 through 140
      Proline residue:  B 129  - end of helix
    Processing helix  chain 'B' and resid 147 through 166
    Processing helix  chain 'B' and resid 170 through 189
    Processing helix  chain 'B' and resid 192 through 202
      removed outlier: 3.847A  pdb=" N   ILE B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 233
      removed outlier: 3.722A  pdb=" N   LYS B 216 " --> pdb=" O   LEU B 212 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   PHE B 232 " --> pdb=" O   MET B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 250
      No H-bonds generated for 'chain 'B' and resid 248 through 250'
    Processing helix  chain 'B' and resid 251 through 285
      removed outlier: 4.030A  pdb=" N   TYR B 255 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU B 256 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      Proline residue:  B 267  - end of helix
      removed outlier: 3.507A  pdb=" N   ARG B 282 " --> pdb=" O   ASP B 278 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   VAL B 283 " --> pdb=" O   LEU B 279 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   HIS B 284 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 305
    Processing helix  chain 'B' and resid 309 through 313
      removed outlier: 3.594A  pdb=" N   SER B 313 " --> pdb=" O   PRO B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 325
      removed outlier: 4.193A  pdb=" N   ILE B 322 " --> pdb=" O   ASN B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 349
    Processing helix  chain 'B' and resid 356 through 379
      removed outlier: 3.549A  pdb=" N   VAL B 376 " --> pdb=" O   GLY B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 383
      removed outlier: 3.556A  pdb=" N   HIS B 383 " --> pdb=" O   PRO B 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 380 through 383'
    Processing helix  chain 'B' and resid 387 through 395
      removed outlier: 3.698A  pdb=" N   GLY B 395 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 401
    Processing helix  chain 'B' and resid 404 through 417
    Processing helix  chain 'B' and resid 421 through 439
    Processing helix  chain 'B' and resid 443 through 460

    508 hydrogen bonds defined for protein.
    1509 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.81

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1051
        1.31 -     1.43: 1785
        1.43 -     1.56: 3986
        1.56 -     1.68: 0
        1.68 -     1.81: 76
  Bond restraints: 6898
  Sorted by residual:
  bond pdb=" C   LEU B 411 "
       pdb=" O   LEU B 411 "
    ideal  model  delta    sigma   weight residual
    1.236  1.186  0.050 1.15e-02 7.56e+03 1.91e+01
  bond pdb=" CA  LEU B 411 "
       pdb=" C   LEU B 411 "
    ideal  model  delta    sigma   weight residual
    1.524  1.472  0.052 1.27e-02 6.20e+03 1.66e+01
  bond pdb=" C   ILE B 410 "
       pdb=" N   LEU B 411 "
    ideal  model  delta    sigma   weight residual
    1.334  1.290  0.045 1.27e-02 6.20e+03 1.24e+01
  bond pdb=" N   LEU B 411 "
       pdb=" CA  LEU B 411 "
    ideal  model  delta    sigma   weight residual
    1.459  1.420  0.040 1.19e-02 7.06e+03 1.10e+01
  bond pdb=" CA  LEU B 411 "
       pdb=" CB  LEU B 411 "
    ideal  model  delta    sigma   weight residual
    1.529  1.505  0.024 1.55e-02 4.16e+03 2.37e+00
  ... (remaining 6893 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 9063
        1.99 -     3.99: 243
        3.99 -     5.98: 38
        5.98 -     7.97: 15
        7.97 -     9.97: 1
  Bond angle restraints: 9360
  Sorted by residual:
  angle pdb=" C   LEU A 319 "
        pdb=" N   ILE A 320 "
        pdb=" CA  ILE A 320 "
      ideal   model   delta    sigma   weight residual
     120.24  124.21   -3.97 6.30e-01 2.52e+00 3.96e+01
  angle pdb=" N   VAL B 241 "
        pdb=" CA  VAL B 241 "
        pdb=" C   VAL B 241 "
      ideal   model   delta    sigma   weight residual
     110.05  106.92    3.13 1.09e+00 8.42e-01 8.24e+00
  angle pdb=" CA  LEU B 411 "
        pdb=" CB  LEU B 411 "
        pdb=" CG  LEU B 411 "
      ideal   model   delta    sigma   weight residual
     116.30  126.27   -9.97 3.50e+00 8.16e-02 8.11e+00
  angle pdb=" N   TYR A  75 "
        pdb=" CA  TYR A  75 "
        pdb=" C   TYR A  75 "
      ideal   model   delta    sigma   weight residual
     109.81  115.86   -6.05 2.21e+00 2.05e-01 7.50e+00
  angle pdb=" N   TYR B  75 "
        pdb=" CA  TYR B  75 "
        pdb=" C   TYR B  75 "
      ideal   model   delta    sigma   weight residual
     109.81  115.59   -5.78 2.21e+00 2.05e-01 6.83e+00
  ... (remaining 9355 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 3606
       17.66 -    35.31: 354
       35.31 -    52.97: 44
       52.97 -    70.63: 9
       70.63 -    88.28: 3
  Dihedral angle restraints: 4016
    sinusoidal: 1528
      harmonic: 2488
  Sorted by residual:
  dihedral pdb=" CA  ASP B 240 "
           pdb=" C   ASP B 240 "
           pdb=" N   VAL B 241 "
           pdb=" CA  VAL B 241 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.89   22.11     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  ALA B 188 "
           pdb=" C   ALA B 188 "
           pdb=" N   ALA B 189 "
           pdb=" CA  ALA B 189 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.40   21.60     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  ASP A 240 "
           pdb=" C   ASP A 240 "
           pdb=" N   VAL A 241 "
           pdb=" CA  VAL A 241 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.75   20.25     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 4013 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 650
       0.037 -    0.074: 346
       0.074 -    0.111: 81
       0.111 -    0.149: 20
       0.149 -    0.186: 3
  Chirality restraints: 1100
  Sorted by residual:
  chirality pdb=" CB  ILE A 356 "
            pdb=" CA  ILE A 356 "
            pdb=" CG1 ILE A 356 "
            pdb=" CG2 ILE A 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.61e-01
  chirality pdb=" CA  LEU B 411 "
            pdb=" N   LEU B 411 "
            pdb=" C   LEU B 411 "
            pdb=" CB  LEU B 411 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.74e-01
  chirality pdb=" CB  ILE B 356 "
            pdb=" CA  ILE B 356 "
            pdb=" CG1 ILE B 356 "
            pdb=" CG2 ILE B 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.67e-01
  ... (remaining 1097 not shown)

  Planarity restraints: 1176
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 149 "    0.050 5.00e-02 4.00e+02   7.60e-02 9.25e+00
        pdb=" N   PRO A 150 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A 150 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 150 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 149 "    0.046 5.00e-02 4.00e+02   7.00e-02 7.84e+00
        pdb=" N   PRO B 150 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO B 150 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 150 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 358 "   -0.045 5.00e-02 4.00e+02   6.67e-02 7.13e+00
        pdb=" N   PRO B 359 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO B 359 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 359 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 1173 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1970
        2.80 -     3.33: 6169
        3.33 -     3.85: 12027
        3.85 -     4.38: 15075
        4.38 -     4.90: 24614
  Nonbonded interactions: 59855
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  54 "
            pdb=" O   HOH A 601 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OH  TYR A  94 "
            pdb=" OG  SER A 350 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   LEU A 397 "
            pdb=" OG  SER A 401 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OG1 THR B 344 "
            pdb=" O   HOH B 601 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" O   ARG A 147 "
            pdb=" OG1 THR A 151 "
     model   vdw
     2.325 3.040
  ... (remaining 59850 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             3.410
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.960
  Find NCS groups from input model:        0.060
  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:             0.010
  Load rotamer database and sin/cos tables:6.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
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      :  0.005   0.071   6900  Z= 0.230
  Angle     :  0.805   9.965   9364  Z= 0.430
  Chirality :  0.046   0.186   1100
  Planarity :  0.008   0.076   1176
  Dihedral  : 13.672  88.284   2438
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.58 (0.17), residues: 896
  helix: -3.85 (0.09), residues: 668
  sheet:  None (None), residues: 0
  loop : -2.25 (0.34), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 340 
 TYR   0.011   0.002   TYR A 419 
 PHE   0.015   0.002   PHE B 357 
 TRP   0.004   0.001   TRP A 253 
 HIS   0.002   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 ( 6898)
  covalent geometry    : angle       0.80316 ( 9360)
  SS BOND              : bond        0.00727 (    2)
  SS BOND              : angle       2.93100 (    4)
  hydrogen bonds       : bond        0.26359 (  508)
  hydrogen bonds       : angle      10.30709 ( 1509)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A   17 ARG cc_start: 0.7241 (ttp80) cc_final: 0.6374 (tpt-90)
REVERT: B   19 ARG cc_start: 0.7478 (mtt-85) cc_final: 0.7243 (mtt-85)
REVERT: B  172 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6085 (tm-30)
REVERT: B  174 ARG cc_start: 0.8239 (ttp-170) cc_final: 0.8015 (ttm170)
REVERT: B  282 ARG cc_start: 0.7735 (mtp-110) cc_final: 0.7483 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.6470
  time to fit residues: 86.4308
Evaluate side-chains
  102 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN
A 270 ASN
A 284 HIS
A 327 ASN
A 418 ASN
A 460 GLN
B 157 ASN
B 270 ASN
B 284 HIS
B 287 ASN
B 327 ASN
B 418 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.127825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.100174 restraints weight = 6781.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 1.44
r_work: 0.3019 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6900  Z= 0.172
  Angle     :  0.590   5.661   9364  Z= 0.297
  Chirality :  0.040   0.129   1100
  Planarity :  0.006   0.064   1176
  Dihedral  :  4.709  20.088    960
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.50 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.46 (0.24), residues: 896
  helix: -0.62 (0.17), residues: 680
  sheet:  None (None), residues: 0
  loop : -1.64 (0.37), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 147 
 TYR   0.008   0.001   TYR A 210 
 PHE   0.023   0.002   PHE B 357 
 TRP   0.006   0.001   TRP A 291 
 HIS   0.002   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 6898)
  covalent geometry    : angle       0.58966 ( 9360)
  SS BOND              : bond        0.00783 (    2)
  SS BOND              : angle       1.00739 (    4)
  hydrogen bonds       : bond        0.04857 (  508)
  hydrogen bonds       : angle       4.81463 ( 1509)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A   15 ARG cc_start: 0.6652 (ttm170) cc_final: 0.6269 (tpt170)
REVERT: A   17 ARG cc_start: 0.6183 (ttp80) cc_final: 0.5083 (tpt-90)
REVERT: A  205 ARG cc_start: 0.6537 (ttp-110) cc_final: 0.6175 (ttp-110)
REVERT: A  276 MET cc_start: 0.8798 (mmm) cc_final: 0.8455 (mmm)
REVERT: A  360 MET cc_start: 0.8515 (mtt) cc_final: 0.8280 (mtt)
REVERT: B  172 GLU cc_start: 0.6893 (tm-30) cc_final: 0.5681 (tm-30)
REVERT: B  174 ARG cc_start: 0.7986 (ttp-170) cc_final: 0.7550 (ttm170)
REVERT: B  282 ARG cc_start: 0.7773 (mtp-110) cc_final: 0.6982 (mtt180)
  outliers start: 11
  outliers final: 6
  residues processed: 107
  average time/residue: 0.8356
  time to fit residues: 92.7557
Evaluate side-chains
  98 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  293 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0050
   chunk 68 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
A 207 GLN
** B 460 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 = 0.3492 r_free = 0.3492 target = 0.128521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.101409 restraints weight = 6807.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 1.42
r_work: 0.3032 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6900  Z= 0.139
  Angle     :  0.525   5.655   9364  Z= 0.262
  Chirality :  0.039   0.124   1100
  Planarity :  0.005   0.058   1176
  Dihedral  :  4.389  18.895    960
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 12.24 %
    Favored  : 86.28 %
  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:  0.49 (0.27), residues: 896
  helix:  0.92 (0.19), residues: 684
  sheet:  None (None), residues: 0
  loop : -1.50 (0.37), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 174 
 TYR   0.007   0.001   TYR B  94 
 PHE   0.022   0.001   PHE B 357 
 TRP   0.004   0.001   TRP B 124 
 HIS   0.002   0.000   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6898)
  covalent geometry    : angle       0.52437 ( 9360)
  SS BOND              : bond        0.00732 (    2)
  SS BOND              : angle       1.37253 (    4)
  hydrogen bonds       : bond        0.04098 (  508)
  hydrogen bonds       : angle       4.26166 ( 1509)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6524 (ttm170) cc_final: 0.6261 (tpt170)
REVERT: A   17 ARG cc_start: 0.6068 (ttp80) cc_final: 0.4985 (tpt-90)
REVERT: A   20 GLN cc_start: 0.6900 (tm-30) cc_final: 0.5654 (tp40)
REVERT: A  205 ARG cc_start: 0.6505 (ttp-110) cc_final: 0.5496 (ttm170)
REVERT: A  276 MET cc_start: 0.8736 (mmm) cc_final: 0.8436 (mmm)
REVERT: B  172 GLU cc_start: 0.6831 (tm-30) cc_final: 0.5737 (tm-30)
REVERT: B  209 ARG cc_start: 0.6683 (mtp-110) cc_final: 0.5350 (mmp80)
REVERT: B  271 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7846 (ptpt)
REVERT: B  282 ARG cc_start: 0.7770 (mtp-110) cc_final: 0.6944 (mtt180)
  outliers start: 10
  outliers final: 3
  residues processed: 104
  average time/residue: 0.7874
  time to fit residues: 85.2283
Evaluate side-chains
  96 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain B residue  271 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 44 optimal weight:    0.6980
   chunk 87 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 85 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 84 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3480 r_free = 0.3480 target = 0.127590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.100052 restraints weight = 6815.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 1.40
r_work: 0.3014 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6900  Z= 0.159
  Angle     :  0.534   5.361   9364  Z= 0.265
  Chirality :  0.040   0.128   1100
  Planarity :  0.004   0.057   1176
  Dihedral  :  4.333  20.176    960
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.27 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.27), residues: 896
  helix:  1.47 (0.19), residues: 686
  sheet:  None (None), residues: 0
  loop : -1.34 (0.38), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  15 
 TYR   0.007   0.001   TYR B 255 
 PHE   0.024   0.001   PHE B 357 
 TRP   0.005   0.001   TRP B 124 
 HIS   0.002   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 6898)
  covalent geometry    : angle       0.53285 ( 9360)
  SS BOND              : bond        0.00766 (    2)
  SS BOND              : angle       1.49524 (    4)
  hydrogen bonds       : bond        0.04101 (  508)
  hydrogen bonds       : angle       4.13545 ( 1509)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6646 (ttm170) cc_final: 0.6281 (tpt170)
REVERT: A   17 ARG cc_start: 0.6199 (ttp80) cc_final: 0.5059 (tpt-90)
REVERT: A   20 GLN cc_start: 0.6944 (tm-30) cc_final: 0.5648 (tp40)
REVERT: A  205 ARG cc_start: 0.6554 (ttp-110) cc_final: 0.6240 (ttp80)
REVERT: A  276 MET cc_start: 0.8781 (mmm) cc_final: 0.8449 (mmm)
REVERT: B  209 ARG cc_start: 0.6796 (mtp-110) cc_final: 0.5355 (mmp80)
REVERT: B  271 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7939 (ptpt)
REVERT: B  282 ARG cc_start: 0.7828 (mtp-110) cc_final: 0.7008 (mtt180)
REVERT: B  385 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7720 (tt0)
  outliers start: 11
  outliers final: 6
  residues processed: 101
  average time/residue: 0.7957
  time to fit residues: 83.6840
Evaluate side-chains
  99 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  385 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 83 optimal weight:    0.5980
   chunk 73 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 80 optimal weight:    0.5980
   chunk 65 optimal weight:    0.4980
   chunk 82 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 456 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.127483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.100189 restraints weight = 6865.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 1.41
r_work: 0.3017 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6900  Z= 0.147
  Angle     :  0.518   5.299   9364  Z= 0.257
  Chirality :  0.040   0.136   1100
  Planarity :  0.004   0.055   1176
  Dihedral  :  4.248  19.434    960
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 13.13 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.28), residues: 896
  helix:  1.77 (0.19), residues: 686
  sheet:  None (None), residues: 0
  loop : -1.21 (0.39), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 167 
 TYR   0.007   0.001   TYR B 255 
 PHE   0.025   0.001   PHE B 357 
 TRP   0.004   0.001   TRP B 124 
 HIS   0.002   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6898)
  covalent geometry    : angle       0.51760 ( 9360)
  SS BOND              : bond        0.00581 (    2)
  SS BOND              : angle       1.31005 (    4)
  hydrogen bonds       : bond        0.03955 (  508)
  hydrogen bonds       : angle       4.04239 ( 1509)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6709 (ttm170) cc_final: 0.6423 (tpt170)
REVERT: A   17 ARG cc_start: 0.6286 (ttp80) cc_final: 0.5955 (ttp80)
REVERT: A   20 GLN cc_start: 0.7034 (tm-30) cc_final: 0.5691 (tp40)
REVERT: A   21 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.5942 (mm)
REVERT: A   30 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.6829 (ptpp)
REVERT: A  276 MET cc_start: 0.8788 (mmm) cc_final: 0.8451 (mmm)
REVERT: B  209 ARG cc_start: 0.6833 (mtp-110) cc_final: 0.5395 (mmp80)
REVERT: B  271 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7957 (ptpt)
REVERT: B  282 ARG cc_start: 0.7836 (mtp-110) cc_final: 0.6945 (mtt180)
REVERT: B  456 GLN cc_start: 0.7461 (mt0) cc_final: 0.7246 (mt0)
  outliers start: 17
  outliers final: 8
  residues processed: 109
  average time/residue: 0.7652
  time to fit residues: 87.0449
Evaluate side-chains
  100 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   30 LYS
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  271 LYS
Chi-restraints excluded: chain B residue  279 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 41 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 56 optimal weight:    0.1980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3490 r_free = 0.3490 target = 0.128637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.100991 restraints weight = 6857.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 1.42
r_work: 0.3019 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6900  Z= 0.139
  Angle     :  0.512   5.297   9364  Z= 0.254
  Chirality :  0.040   0.130   1100
  Planarity :  0.004   0.054   1176
  Dihedral  :  4.182  18.925    960
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 13.86 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (0.28), residues: 896
  helix:  1.94 (0.19), residues: 686
  sheet:  None (None), residues: 0
  loop : -1.12 (0.39), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  64 
 TYR   0.006   0.001   TYR B 255 
 PHE   0.027   0.001   PHE B 357 
 TRP   0.003   0.001   TRP B 124 
 HIS   0.002   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6898)
  covalent geometry    : angle       0.51120 ( 9360)
  SS BOND              : bond        0.00753 (    2)
  SS BOND              : angle       1.22515 (    4)
  hydrogen bonds       : bond        0.03863 (  508)
  hydrogen bonds       : angle       3.99188 ( 1509)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6705 (ttm170) cc_final: 0.6393 (tpt170)
REVERT: A   17 ARG cc_start: 0.6291 (ttp80) cc_final: 0.5951 (ttp80)
REVERT: A   20 GLN cc_start: 0.7008 (tm-30) cc_final: 0.5663 (tp40)
REVERT: A   21 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.5965 (mm)
REVERT: A  167 ARG cc_start: 0.7153 (mpt180) cc_final: 0.6565 (mpt180)
REVERT: A  276 MET cc_start: 0.8738 (mmm) cc_final: 0.8405 (mmm)
REVERT: B   20 GLN cc_start: 0.5810 (mm110) cc_final: 0.5265 (tp40)
REVERT: B  209 ARG cc_start: 0.6884 (mtp-110) cc_final: 0.5464 (mmp80)
REVERT: B  282 ARG cc_start: 0.7777 (mtp-110) cc_final: 0.6903 (mtt180)
  outliers start: 17
  outliers final: 5
  residues processed: 101
  average time/residue: 0.7432
  time to fit residues: 78.3007
Evaluate side-chains
  94 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain B residue  222 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0870
   chunk 57 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
A 119 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.128022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.100446 restraints weight = 6789.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 1.41
r_work: 0.3018 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6900  Z= 0.149
  Angle     :  0.520   5.255   9364  Z= 0.258
  Chirality :  0.040   0.138   1100
  Planarity :  0.004   0.054   1176
  Dihedral  :  4.189  19.157    960
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 14.31 %
    Favored  : 83.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.27), residues: 896
  helix:  2.01 (0.19), residues: 686
  sheet:  None (None), residues: 0
  loop : -1.05 (0.39), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  64 
 TYR   0.007   0.001   TYR A 210 
 PHE   0.030   0.001   PHE B 357 
 TRP   0.004   0.001   TRP B 124 
 HIS   0.002   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 6898)
  covalent geometry    : angle       0.51925 ( 9360)
  SS BOND              : bond        0.00712 (    2)
  SS BOND              : angle       1.24478 (    4)
  hydrogen bonds       : bond        0.03941 (  508)
  hydrogen bonds       : angle       4.00581 ( 1509)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6635 (ttm170) cc_final: 0.6329 (tpt170)
REVERT: A   17 ARG cc_start: 0.6206 (ttp80) cc_final: 0.5857 (ttp80)
REVERT: A   20 GLN cc_start: 0.6957 (tm-30) cc_final: 0.5623 (tp40)
REVERT: A   21 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.5882 (mm)
REVERT: A  167 ARG cc_start: 0.7085 (mpt180) cc_final: 0.6878 (mpt180)
REVERT: A  276 MET cc_start: 0.8733 (mmm) cc_final: 0.8388 (mmm)
REVERT: B   20 GLN cc_start: 0.5806 (mm110) cc_final: 0.5240 (tp40)
REVERT: B  209 ARG cc_start: 0.6836 (mtp-110) cc_final: 0.5390 (mmp80)
REVERT: B  282 ARG cc_start: 0.7732 (mtp-110) cc_final: 0.6836 (mtt180)
  outliers start: 13
  outliers final: 5
  residues processed: 103
  average time/residue: 0.7237
  time to fit residues: 77.7579
Evaluate side-chains
  95 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain B residue  222 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 11 optimal weight:    0.3980
   chunk 14 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 47 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 80 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3486 r_free = 0.3486 target = 0.128132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.100350 restraints weight = 6816.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 1.43
r_work: 0.3019 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6900  Z= 0.145
  Angle     :  0.520   5.393   9364  Z= 0.258
  Chirality :  0.040   0.146   1100
  Planarity :  0.004   0.053   1176
  Dihedral  :  4.162  18.650    960
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 15.04 %
    Favored  : 83.48 %
  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:  2.08 (0.27), residues: 896
  helix:  2.07 (0.19), residues: 686
  sheet:  None (None), residues: 0
  loop : -1.00 (0.39), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  64 
 TYR   0.007   0.001   TYR A 210 
 PHE   0.032   0.001   PHE B 357 
 TRP   0.003   0.001   TRP B 124 
 HIS   0.002   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 6898)
  covalent geometry    : angle       0.51915 ( 9360)
  SS BOND              : bond        0.00708 (    2)
  SS BOND              : angle       1.24892 (    4)
  hydrogen bonds       : bond        0.03900 (  508)
  hydrogen bonds       : angle       3.99799 ( 1509)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6746 (ttm170) cc_final: 0.6428 (tpt170)
REVERT: A   17 ARG cc_start: 0.6314 (ttp80) cc_final: 0.5967 (ttp80)
REVERT: A   20 GLN cc_start: 0.7047 (tm-30) cc_final: 0.5696 (tp40)
REVERT: A   21 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6023 (mm)
REVERT: A   91 MET cc_start: 0.8455 (mtt) cc_final: 0.8093 (mtt)
REVERT: A  167 ARG cc_start: 0.7172 (mpt180) cc_final: 0.6961 (mpt180)
REVERT: A  276 MET cc_start: 0.8773 (mmm) cc_final: 0.8418 (mmm)
REVERT: B   20 GLN cc_start: 0.5873 (mm110) cc_final: 0.5287 (tp40)
REVERT: B  209 ARG cc_start: 0.6881 (mtp-110) cc_final: 0.5440 (mmp80)
REVERT: B  282 ARG cc_start: 0.7779 (mtp-110) cc_final: 0.6901 (mtt180)
  outliers start: 10
  outliers final: 6
  residues processed: 103
  average time/residue: 0.7580
  time to fit residues: 81.4067
Evaluate side-chains
  97 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue  222 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 50 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0770
   chunk 20 optimal weight:    0.5980
   chunk 88 optimal weight:    0.6980
   overall best weight:    0.5338

-------------------------------------------------------------------------------
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 = 0.3492 r_free = 0.3492 target = 0.128689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.101061 restraints weight = 6777.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 1.42
r_work: 0.3020 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2889 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6900  Z= 0.137
  Angle     :  0.514   5.364   9364  Z= 0.255
  Chirality :  0.040   0.138   1100
  Planarity :  0.004   0.053   1176
  Dihedral  :  4.127  17.400    960
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 15.63 %
    Favored  : 82.89 %
  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:  2.20 (0.28), residues: 896
  helix:  2.16 (0.19), residues: 686
  sheet:  None (None), residues: 0
  loop : -0.95 (0.39), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  64 
 TYR   0.007   0.001   TYR A 210 
 PHE   0.035   0.001   PHE B 357 
 TRP   0.003   0.001   TRP B 124 
 HIS   0.002   0.000   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6898)
  covalent geometry    : angle       0.51323 ( 9360)
  SS BOND              : bond        0.00688 (    2)
  SS BOND              : angle       1.21708 (    4)
  hydrogen bonds       : bond        0.03834 (  508)
  hydrogen bonds       : angle       3.97563 ( 1509)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6746 (ttm170) cc_final: 0.6457 (tpt170)
REVERT: A   17 ARG cc_start: 0.6341 (ttp80) cc_final: 0.6000 (ttp80)
REVERT: A   20 GLN cc_start: 0.7036 (tm-30) cc_final: 0.5679 (tp40)
REVERT: A   21 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6038 (mm)
REVERT: A  167 ARG cc_start: 0.7139 (mpt180) cc_final: 0.6809 (mpt180)
REVERT: B   20 GLN cc_start: 0.5860 (mm110) cc_final: 0.5290 (tp40)
REVERT: B  209 ARG cc_start: 0.6815 (mtp-110) cc_final: 0.5395 (mmp80)
REVERT: B  282 ARG cc_start: 0.7776 (mtp-110) cc_final: 0.6888 (mtt180)
  outliers start: 10
  outliers final: 5
  residues processed: 101
  average time/residue: 0.7673
  time to fit residues: 80.9019
Evaluate side-chains
  99 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue  222 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 80 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 62 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3481 r_free = 0.3481 target = 0.127574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.099816 restraints weight = 6691.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 1.42
r_work: 0.3009 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6900  Z= 0.161
  Angle     :  0.534   5.259   9364  Z= 0.265
  Chirality :  0.041   0.151   1100
  Planarity :  0.004   0.053   1176
  Dihedral  :  4.199  18.357    960
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 16.08 %
    Favored  : 82.74 %
  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:  2.13 (0.27), residues: 896
  helix:  2.10 (0.19), residues: 686
  sheet:  None (None), residues: 0
  loop : -0.97 (0.39), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  64 
 TYR   0.009   0.001   TYR A 210 
 PHE   0.035   0.002   PHE B 357 
 TRP   0.004   0.001   TRP B 124 
 HIS   0.002   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 6898)
  covalent geometry    : angle       0.53337 ( 9360)
  SS BOND              : bond        0.00752 (    2)
  SS BOND              : angle       1.28684 (    4)
  hydrogen bonds       : bond        0.04025 (  508)
  hydrogen bonds       : angle       4.04482 ( 1509)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6745 (ttm170) cc_final: 0.6422 (tpt170)
REVERT: A   17 ARG cc_start: 0.6389 (ttp80) cc_final: 0.6018 (ttp80)
REVERT: A   20 GLN cc_start: 0.7008 (tm-30) cc_final: 0.5656 (tp40)
REVERT: A   21 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6078 (mm)
REVERT: A  167 ARG cc_start: 0.7142 (mpt180) cc_final: 0.6802 (mpt180)
REVERT: B   20 GLN cc_start: 0.5810 (mm110) cc_final: 0.5266 (tp40)
REVERT: B  209 ARG cc_start: 0.6836 (mtp-110) cc_final: 0.5414 (mmp80)
REVERT: B  282 ARG cc_start: 0.7778 (mtp-110) cc_final: 0.6895 (mtt180)
  outliers start: 8
  outliers final: 5
  residues processed: 102
  average time/residue: 0.7544
  time to fit residues: 80.1427
Evaluate side-chains
  99 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain B residue   21 LEU
Chi-restraints excluded: chain B residue  222 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3480 r_free = 0.3480 target = 0.127637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.099864 restraints weight = 6724.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 1.42
r_work: 0.3009 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6900  Z= 0.160
  Angle     :  0.536   5.491   9364  Z= 0.266
  Chirality :  0.041   0.147   1100
  Planarity :  0.004   0.053   1176
  Dihedral  :  4.208  18.447    960
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 16.37 %
    Favored  : 82.60 %
  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:  2.08 (0.27), residues: 896
  helix:  2.09 (0.19), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.09 (0.38), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  64 
 TYR   0.009   0.001   TYR A 210 
 PHE   0.035   0.002   PHE B 357 
 TRP   0.004   0.001   TRP A 291 
 HIS   0.002   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 6898)
  covalent geometry    : angle       0.53575 ( 9360)
  SS BOND              : bond        0.00723 (    2)
  SS BOND              : angle       1.27084 (    4)
  hydrogen bonds       : bond        0.04016 (  508)
  hydrogen bonds       : angle       4.04855 ( 1509)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2451.96 seconds
wall clock time: 42 minutes 31.00 seconds (2551.00 seconds total)