Starting phenix.real_space_refine
on Sat May 10 19:45:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ga5_29890/05_2025/8ga5_29890.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ga5_29890/05_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_29890/05_2025/8ga5_29890.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ga5_29890/05_2025/8ga5_29890.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ga5_29890/05_2025/8ga5_29890.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ga5_29890/05_2025/8ga5_29890.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.86, per 1000 atoms: 0.72
  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: 1.45
  Conformation dependent library (CDL) restraints added in 939.1 milliseconds
  

  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: 0.65
  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: 1.96

  Time building geometry restraints manager: 1.74 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: 0.03
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:             2.680
  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:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.930
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  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:11.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.410
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.58 (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
 TRP   0.004   0.001   TRP A 253 
 HIS   0.002   0.001   HIS B 234 
 PHE   0.015   0.002   PHE B 357 
 TYR   0.011   0.002   TYR A 419 
 ARG   0.006   0.000   ARG B 340 

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

*********************** 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  : 0.664 
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: 1.3618
  time to fit residues: 182.2673
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  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 68 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   chunk 23 optimal weight:    0.1980
   chunk 46 optimal weight:    0.0060
   chunk 36 optimal weight:    0.1980
   chunk 70 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0870
   chunk 42 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.2374

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN
A 207 GLN
A 270 ASN
** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3530 r_free = 0.3530 target = 0.131331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.104566 restraints weight = 6715.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 1.40
r_work: 0.3085 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6900  Z= 0.125
  Angle     :  0.551   5.943   9364  Z= 0.278
  Chirality :  0.038   0.122   1100
  Planarity :  0.006   0.060   1176
  Dihedral  :  4.534  16.767    960
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 11.21 %
    Favored  : 87.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.24), residues: 896
  helix: -0.48 (0.17), residues: 682
  sheet:  None (None), residues: 0
  loop : -1.87 (0.35), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 291 
 HIS   0.002   0.001   HIS A 281 
 PHE   0.024   0.001   PHE B 357 
 TYR   0.007   0.001   TYR B  94 
 ARG   0.002   0.000   ARG B 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04395 (  508)
  hydrogen bonds       : angle       4.67360 ( 1509)
  SS BOND              : bond        0.00814 (    2)
  SS BOND              : angle       0.82752 (    4)
  covalent geometry    : bond        0.00257 ( 6898)
  covalent geometry    : angle       0.55109 ( 9360)

*********************** 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: 9
    poor density    : 102
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6578 (ttm170) cc_final: 0.6317 (tpt170)
REVERT: A   17 ARG cc_start: 0.6092 (ttp80) cc_final: 0.4984 (tpt-90)
REVERT: A   20 GLN cc_start: 0.6719 (tm-30) cc_final: 0.5565 (tp40)
REVERT: A  276 MET cc_start: 0.8755 (mmm) cc_final: 0.8430 (mmm)
REVERT: A  373 MET cc_start: 0.8146 (mtp) cc_final: 0.7772 (mtt)
REVERT: B   19 ARG cc_start: 0.6158 (mtt-85) cc_final: 0.5780 (mtt-85)
REVERT: B  172 GLU cc_start: 0.6764 (tm-30) cc_final: 0.5597 (tm-30)
REVERT: B  174 ARG cc_start: 0.7979 (ttp-170) cc_final: 0.7562 (ttm170)
REVERT: B  209 ARG cc_start: 0.6865 (mtp-110) cc_final: 0.5574 (mmp80)
REVERT: B  282 ARG cc_start: 0.7793 (mtp-110) cc_final: 0.6955 (mtt180)
  outliers start: 9
  outliers final: 4
  residues processed: 108
  average time/residue: 1.5361
  time to fit residues: 172.9458
Evaluate side-chains
  94 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 GLU
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 33 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 70 optimal weight:    0.7980
   chunk 64 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0870
   chunk 62 optimal weight:    0.6980
   chunk 59 optimal weight:    0.5980
   chunk 66 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.128925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.101638 restraints weight = 6809.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 1.44
r_work: 0.3027 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.2092

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= 0.143
  Angle     :  0.524   5.448   9364  Z= 0.261
  Chirality :  0.039   0.129   1100
  Planarity :  0.005   0.058   1176
  Dihedral  :  4.322  18.632    960
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 12.54 %
    Favored  : 85.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.27), residues: 896
  helix:  0.99 (0.19), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.48 (0.38), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 291 
 HIS   0.002   0.001   HIS B 234 
 PHE   0.027   0.001   PHE B 357 
 TYR   0.007   0.001   TYR A 100 
 ARG   0.002   0.000   ARG A 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04110 (  508)
  hydrogen bonds       : angle       4.21785 ( 1509)
  SS BOND              : bond        0.00895 (    2)
  SS BOND              : angle       1.35924 (    4)
  covalent geometry    : bond        0.00329 ( 6898)
  covalent geometry    : angle       0.52323 ( 9360)

*********************** 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
  109 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6604 (ttm170) cc_final: 0.6377 (tpt170)
REVERT: A   17 ARG cc_start: 0.6089 (ttp80) cc_final: 0.5014 (tpt-90)
REVERT: A   20 GLN cc_start: 0.6803 (tm-30) cc_final: 0.5577 (tp40)
REVERT: A  205 ARG cc_start: 0.6552 (ttp-110) cc_final: 0.6189 (ttp80)
REVERT: A  276 MET cc_start: 0.8730 (mmm) cc_final: 0.8423 (mmm)
REVERT: B  172 GLU cc_start: 0.6847 (tm-30) cc_final: 0.5762 (tm-30)
REVERT: B  209 ARG cc_start: 0.6694 (mtp-110) cc_final: 0.5352 (mmp80)
REVERT: B  271 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7905 (ptpt)
REVERT: B  282 ARG cc_start: 0.7757 (mtp-110) cc_final: 0.6899 (mtt180)
  outliers start: 12
  outliers final: 5
  residues processed: 103
  average time/residue: 1.5221
  time to fit residues: 163.5705
Evaluate side-chains
  96 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
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   21 LEU
Chi-restraints excluded: chain B residue  222 VAL
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 66 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 77 optimal weight:    0.1980
   chunk 70 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 284 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.128481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.100646 restraints weight = 6782.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 1.43
r_work: 0.3021 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6900  Z= 0.150
  Angle     :  0.521   5.478   9364  Z= 0.259
  Chirality :  0.040   0.128   1100
  Planarity :  0.004   0.056   1176
  Dihedral  :  4.257  19.107    960
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.86 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.28), residues: 896
  helix:  1.54 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop : -1.26 (0.38), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 124 
 HIS   0.002   0.001   HIS B 234 
 PHE   0.025   0.001   PHE B 357 
 TYR   0.007   0.001   TYR B  94 
 ARG   0.002   0.000   ARG B  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04008 (  508)
  hydrogen bonds       : angle       4.09589 ( 1509)
  SS BOND              : bond        0.00770 (    2)
  SS BOND              : angle       1.42849 (    4)
  covalent geometry    : bond        0.00351 ( 6898)
  covalent geometry    : angle       0.52023 ( 9360)

*********************** 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
  109 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6697 (ttm170) cc_final: 0.6382 (tpt170)
REVERT: A   17 ARG cc_start: 0.6275 (ttp80) cc_final: 0.5152 (tpt-90)
REVERT: A   20 GLN cc_start: 0.6882 (tm-30) cc_final: 0.5635 (tp40)
REVERT: A  205 ARG cc_start: 0.6584 (ttp-110) cc_final: 0.6220 (ttp80)
REVERT: A  276 MET cc_start: 0.8756 (mmm) cc_final: 0.8430 (mmm)
REVERT: B  209 ARG cc_start: 0.6870 (mtp-110) cc_final: 0.5462 (mmp80)
REVERT: B  271 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7947 (ptpt)
REVERT: B  282 ARG cc_start: 0.7843 (mtp-110) cc_final: 0.6990 (mtt180)
  outliers start: 11
  outliers final: 5
  residues processed: 104
  average time/residue: 1.5475
  time to fit residues: 167.5594
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  : 0.645 
-------------------------------------------------------------------------------
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   21 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  271 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0670
   chunk 83 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.5518

-------------------------------------------------------------------------------
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 = 0.3495 r_free = 0.3495 target = 0.129101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.101416 restraints weight = 6772.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 1.42
r_work: 0.3027 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.2331

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     :  0.506   5.466   9364  Z= 0.251
  Chirality :  0.039   0.125   1100
  Planarity :  0.004   0.054   1176
  Dihedral  :  4.162  18.319    960
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 14.45 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.28), residues: 896
  helix:  1.84 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop : -1.10 (0.39), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 124 
 HIS   0.002   0.000   HIS B 234 
 PHE   0.026   0.001   PHE B 357 
 TYR   0.006   0.001   TYR B 255 
 ARG   0.002   0.000   ARG B  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03856 (  508)
  hydrogen bonds       : angle       3.99886 ( 1509)
  SS BOND              : bond        0.00682 (    2)
  SS BOND              : angle       1.20983 (    4)
  covalent geometry    : bond        0.00317 ( 6898)
  covalent geometry    : angle       0.50525 ( 9360)

*********************** 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
  105 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6694 (ttm170) cc_final: 0.6403 (tpt170)
REVERT: A   17 ARG cc_start: 0.6330 (ttp80) cc_final: 0.6008 (ttp80)
REVERT: A   20 GLN cc_start: 0.6890 (tm-30) cc_final: 0.5627 (tp40)
REVERT: A   21 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.5947 (mm)
REVERT: A   30 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.6786 (ptpp)
REVERT: A  276 MET cc_start: 0.8730 (mmm) cc_final: 0.8400 (mmm)
REVERT: B  209 ARG cc_start: 0.6868 (mtp-110) cc_final: 0.5461 (mmp80)
REVERT: B  271 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7933 (ptpt)
REVERT: B  282 ARG cc_start: 0.7782 (mtp-110) cc_final: 0.6916 (mtt180)
REVERT: B  456 GLN cc_start: 0.7412 (mt0) cc_final: 0.7200 (mt0)
  outliers start: 12
  outliers final: 5
  residues processed: 100
  average time/residue: 1.4918
  time to fit residues: 155.7880
Evaluate side-chains
  93 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
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  222 VAL
Chi-restraints excluded: chain B residue  271 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0870
   chunk 10 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.8560

-------------------------------------------------------------------------------
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 = 0.3473 r_free = 0.3473 target = 0.127043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.099179 restraints weight = 6722.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 1.42
r_work: 0.3000 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.2328

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= 0.173
  Angle     :  0.536   5.316   9364  Z= 0.267
  Chirality :  0.041   0.131   1100
  Planarity :  0.004   0.055   1176
  Dihedral  :  4.254  19.877    960
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.01 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.27), residues: 896
  helix:  1.83 (0.19), residues: 686
  sheet:  None (None), residues: 0
  loop : -1.06 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 124 
 HIS   0.003   0.001   HIS B 234 
 PHE   0.029   0.002   PHE B 357 
 TYR   0.009   0.001   TYR A 210 
 ARG   0.002   0.000   ARG A 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04111 (  508)
  hydrogen bonds       : angle       4.09053 ( 1509)
  SS BOND              : bond        0.00770 (    2)
  SS BOND              : angle       1.34374 (    4)
  covalent geometry    : bond        0.00416 ( 6898)
  covalent geometry    : angle       0.53574 ( 9360)

*********************** 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: 15
    poor density    : 92
  time to evaluate  : 0.664 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6719 (ttm170) cc_final: 0.6363 (tpt170)
REVERT: A   17 ARG cc_start: 0.6271 (ttp80) cc_final: 0.5939 (ttp80)
REVERT: A   20 GLN cc_start: 0.6896 (tm-30) cc_final: 0.5609 (tp40)
REVERT: A   21 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.5997 (mm)
REVERT: A   30 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6740 (ptpp)
REVERT: A  167 ARG cc_start: 0.7166 (mpt180) cc_final: 0.6575 (mpt180)
REVERT: A  209 ARG cc_start: 0.5853 (mpt-90) cc_final: 0.5240 (mmt180)
REVERT: A  276 MET cc_start: 0.8780 (mmm) cc_final: 0.8403 (mmm)
REVERT: B   20 GLN cc_start: 0.5812 (mm110) cc_final: 0.5341 (tp40)
REVERT: B  209 ARG cc_start: 0.6808 (mtp-110) cc_final: 0.5364 (mmp80)
REVERT: B  271 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7922 (ptpt)
REVERT: B  282 ARG cc_start: 0.7803 (mtp-110) cc_final: 0.6935 (mtt180)
  outliers start: 15
  outliers final: 6
  residues processed: 102
  average time/residue: 1.5564
  time to fit residues: 165.3324
Evaluate side-chains
  97 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
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  271 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3479 r_free = 0.3479 target = 0.127483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.099621 restraints weight = 6702.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 1.42
r_work: 0.3005 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2873 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6900  Z= 0.161
  Angle     :  0.527   5.361   9364  Z= 0.262
  Chirality :  0.040   0.126   1100
  Planarity :  0.004   0.055   1176
  Dihedral  :  4.225  19.497    960
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 14.16 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.27), residues: 896
  helix:  1.93 (0.19), residues: 686
  sheet:  None (None), residues: 0
  loop : -1.07 (0.39), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 124 
 HIS   0.002   0.001   HIS B 234 
 PHE   0.028   0.001   PHE B 357 
 TYR   0.008   0.001   TYR A 210 
 ARG   0.002   0.000   ARG A 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04019 (  508)
  hydrogen bonds       : angle       4.05970 ( 1509)
  SS BOND              : bond        0.00753 (    2)
  SS BOND              : angle       1.32472 (    4)
  covalent geometry    : bond        0.00383 ( 6898)
  covalent geometry    : angle       0.52624 ( 9360)

*********************** 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
  103 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6715 (ttm170) cc_final: 0.6380 (tpt170)
REVERT: A   17 ARG cc_start: 0.6247 (ttp80) cc_final: 0.5894 (ttp80)
REVERT: A   21 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6019 (mm)
REVERT: A  167 ARG cc_start: 0.7129 (mpt180) cc_final: 0.6928 (mpt180)
REVERT: A  276 MET cc_start: 0.8751 (mmm) cc_final: 0.8386 (mmm)
REVERT: B   20 GLN cc_start: 0.5821 (mm110) cc_final: 0.5299 (tp40)
REVERT: B  209 ARG cc_start: 0.6876 (mtp-110) cc_final: 0.5430 (mmp80)
REVERT: B  282 ARG cc_start: 0.7760 (mtp-110) cc_final: 0.6880 (mtt180)
  outliers start: 13
  outliers final: 7
  residues processed: 97
  average time/residue: 1.4324
  time to fit residues: 145.1556
Evaluate side-chains
  94 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain B residue  238 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 80 optimal weight:    0.5980
   chunk 29 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9990
   chunk 56 optimal weight:    0.3980
   chunk 19 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0970
   chunk 15 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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 = 0.3498 r_free = 0.3498 target = 0.129073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.101569 restraints weight = 6709.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 1.41
r_work: 0.3027 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6900  Z= 0.128
  Angle     :  0.500   5.745   9364  Z= 0.248
  Chirality :  0.039   0.124   1100
  Planarity :  0.004   0.053   1176
  Dihedral  :  4.080  17.495    960
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 15.04 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.28), residues: 896
  helix:  2.14 (0.19), residues: 686
  sheet:  None (None), residues: 0
  loop : -0.95 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 124 
 HIS   0.002   0.000   HIS B 234 
 PHE   0.031   0.001   PHE B 357 
 TYR   0.006   0.001   TYR B  94 
 ARG   0.002   0.000   ARG B  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03741 (  508)
  hydrogen bonds       : angle       3.94106 ( 1509)
  SS BOND              : bond        0.00619 (    2)
  SS BOND              : angle       1.18490 (    4)
  covalent geometry    : bond        0.00289 ( 6898)
  covalent geometry    : angle       0.49919 ( 9360)

*********************** 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
  103 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6680 (ttm170) cc_final: 0.6389 (tpt170)
REVERT: A   20 GLN cc_start: 0.7004 (tm-30) cc_final: 0.5687 (tp40)
REVERT: A  167 ARG cc_start: 0.7157 (mpt180) cc_final: 0.6955 (mpt180)
REVERT: A  457 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7198 (tp30)
REVERT: B   20 GLN cc_start: 0.5804 (mm110) cc_final: 0.5288 (tp40)
REVERT: B  209 ARG cc_start: 0.6818 (mtp-110) cc_final: 0.5391 (mmp80)
REVERT: B  282 ARG cc_start: 0.7766 (mtp-110) cc_final: 0.6886 (mtt180)
  outliers start: 9
  outliers final: 4
  residues processed: 100
  average time/residue: 1.4740
  time to fit residues: 153.8285
Evaluate side-chains
  92 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 79 optimal weight:    0.0980
   chunk 56 optimal weight:    0.2980
   chunk 76 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 63 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.3499 r_free = 0.3499 target = 0.129185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.101462 restraints weight = 6721.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.43
r_work: 0.3035 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6900  Z= 0.131
  Angle     :  0.504   5.612   9364  Z= 0.250
  Chirality :  0.039   0.124   1100
  Planarity :  0.004   0.053   1176
  Dihedral  :  4.055  16.883    960
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 16.08 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.28), residues: 896
  helix:  2.19 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.95 (0.40), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 124 
 HIS   0.002   0.000   HIS B 234 
 PHE   0.036   0.001   PHE B 357 
 TYR   0.007   0.001   TYR A 210 
 ARG   0.002   0.000   ARG A  17 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03748 (  508)
  hydrogen bonds       : angle       3.93183 ( 1509)
  SS BOND              : bond        0.00645 (    2)
  SS BOND              : angle       1.21107 (    4)
  covalent geometry    : bond        0.00300 ( 6898)
  covalent geometry    : angle       0.50340 ( 9360)

*********************** 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
  99 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6682 (ttm170) cc_final: 0.6415 (tpt170)
REVERT: A   20 GLN cc_start: 0.7001 (tm-30) cc_final: 0.5658 (tp40)
REVERT: A  167 ARG cc_start: 0.7148 (mpt180) cc_final: 0.6812 (mpt180)
REVERT: A  457 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7203 (tp30)
REVERT: B   20 GLN cc_start: 0.5804 (mm110) cc_final: 0.5281 (tp40)
REVERT: B  209 ARG cc_start: 0.6821 (mtp-110) cc_final: 0.5401 (mmp80)
REVERT: B  282 ARG cc_start: 0.7800 (mtp-110) cc_final: 0.6901 (mtt180)
  outliers start: 7
  outliers final: 4
  residues processed: 97
  average time/residue: 1.5652
  time to fit residues: 158.4126
Evaluate side-chains
  93 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 89
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
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 B residue  222 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 68 optimal weight:    0.2980
   chunk 48 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.3457 r_free = 0.3457 target = 0.125692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.097660 restraints weight = 6841.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 1.42
r_work: 0.2973 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.2841 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6900  Z= 0.215
  Angle     :  0.580   5.461   9364  Z= 0.288
  Chirality :  0.044   0.144   1100
  Planarity :  0.005   0.053   1176
  Dihedral  :  4.355  20.690    960
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.27), residues: 896
  helix:  1.94 (0.19), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.17 (0.38), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 291 
 HIS   0.003   0.001   HIS B 234 
 PHE   0.035   0.002   PHE B 357 
 TYR   0.013   0.002   TYR A 210 
 ARG   0.003   0.000   ARG A 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04363 (  508)
  hydrogen bonds       : angle       4.18842 ( 1509)
  SS BOND              : bond        0.00891 (    2)
  SS BOND              : angle       1.49582 (    4)
  covalent geometry    : bond        0.00527 ( 6898)
  covalent geometry    : angle       0.57904 ( 9360)

********************** 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
  101 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6072 (mm)
REVERT: A  167 ARG cc_start: 0.7172 (mpt180) cc_final: 0.6823 (mpt180)
REVERT: A  209 ARG cc_start: 0.5907 (mpt-90) cc_final: 0.5244 (mmt180)
REVERT: B   20 GLN cc_start: 0.5866 (mm110) cc_final: 0.5355 (tp40)
REVERT: B  282 ARG cc_start: 0.7836 (mtp-110) cc_final: 0.6944 (mtt180)
  outliers start: 8
  outliers final: 5
  residues processed: 100
  average time/residue: 1.5627
  time to fit residues: 163.0448
Evaluate side-chains
  97 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
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  138 THR
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  235 GLU
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 68 optimal weight:    0.5980
   chunk 69 optimal weight:    0.0030
   chunk 87 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0000
   chunk 2 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0980
   chunk 48 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 31 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0980
   overall best weight:    0.1594

-------------------------------------------------------------------------------
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 = 0.3530 r_free = 0.3530 target = 0.131621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.104685 restraints weight = 6699.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 1.41
r_work: 0.3070 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6900  Z= 0.107
  Angle     :  0.489   6.056   9364  Z= 0.242
  Chirality :  0.038   0.122   1100
  Planarity :  0.004   0.053   1176
  Dihedral  :  3.972  14.333    960
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 16.96 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.28), residues: 896
  helix:  2.33 (0.19), residues: 686
  sheet:  None (None), residues: 0
  loop : -0.86 (0.39), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 272 
 HIS   0.002   0.001   HIS B 234 
 PHE   0.032   0.001   PHE B 357 
 TYR   0.007   0.001   TYR B  94 
 ARG   0.007   0.000   ARG A  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03503 (  508)
  hydrogen bonds       : angle       3.86650 ( 1509)
  SS BOND              : bond        0.00492 (    2)
  SS BOND              : angle       1.03227 (    4)
  covalent geometry    : bond        0.00220 ( 6898)
  covalent geometry    : angle       0.48852 ( 9360)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4852.30 seconds
wall clock time: 84 minutes 18.50 seconds (5058.50 seconds total)