Starting phenix.real_space_refine
on Tue Mar 11 22:45:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ga5_29890/03_2025/8ga5_29890.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ga5_29890/03_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_29890/03_2025/8ga5_29890.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ga5_29890/03_2025/8ga5_29890.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ga5_29890/03_2025/8ga5_29890.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ga5_29890/03_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.03, per 1000 atoms: 0.74
  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: 1.42
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.64
  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: 2.03

  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:             2.080
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     20.160
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  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:15.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.140
-------------------------------------------------------------------------------
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   6898  Z= 0.337
  Angle     :  0.803   9.965   9360  Z= 0.429
  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 

*********************** 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  : 0.696 
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: 1.5004
  time to fit residues: 200.6899
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  : 0.684 
-------------------------------------------------------------------------------
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 = 0.131329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.104568 restraints weight = 6715.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 1.40
r_work: 0.3084 rms_B_bonded: 2.09 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: 0.8099
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   6898  Z= 0.167
  Angle     :  0.551   5.943   9360  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 

*********************** 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  : 0.713 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6576 (ttm170) cc_final: 0.6314 (tpt170)
REVERT: A   17 ARG cc_start: 0.6090 (ttp80) cc_final: 0.4982 (tpt-90)
REVERT: A   20 GLN cc_start: 0.6717 (tm-30) cc_final: 0.5564 (tp40)
REVERT: A  276 MET cc_start: 0.8754 (mmm) cc_final: 0.8428 (mmm)
REVERT: A  373 MET cc_start: 0.8145 (mtp) cc_final: 0.7771 (mtt)
REVERT: B   19 ARG cc_start: 0.6155 (mtt-85) cc_final: 0.5777 (mtt-85)
REVERT: B  172 GLU cc_start: 0.6764 (tm-30) cc_final: 0.5597 (tm-30)
REVERT: B  174 ARG cc_start: 0.7978 (ttp-170) cc_final: 0.7561 (ttm170)
REVERT: B  209 ARG cc_start: 0.6864 (mtp-110) cc_final: 0.5573 (mmp80)
REVERT: B  282 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.6954 (mtt180)
  outliers start: 9
  outliers final: 4
  residues processed: 108
  average time/residue: 1.5835
  time to fit residues: 178.1225
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  : 0.784 
-------------------------------------------------------------------------------
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:    0.9990
   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:    0.0770
   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:    0.5538

-------------------------------------------------------------------------------
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 = 0.3503 r_free = 0.3503 target = 0.129616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.101885 restraints weight = 6789.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 1.44
r_work: 0.3028 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6898  Z= 0.210
  Angle     :  0.523   5.462   9360  Z= 0.261
  Chirality :  0.039   0.129   1100
  Planarity :  0.005   0.057   1176
  Dihedral  :  4.336  17.979    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 :  1.77 %
    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:  0.56 (0.27), residues: 896
  helix:  0.98 (0.19), residues: 684
  sheet:  None (None), residues: 0
  loop : -1.49 (0.37), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   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 

*********************** 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: 12
    poor density    : 96
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6566 (ttm170) cc_final: 0.6328 (tpt170)
REVERT: A   17 ARG cc_start: 0.6029 (ttp80) cc_final: 0.4979 (tpt-90)
REVERT: A   20 GLN cc_start: 0.6781 (tm-30) cc_final: 0.5559 (tp40)
REVERT: A  205 ARG cc_start: 0.6510 (ttp-110) cc_final: 0.5479 (ttm170)
REVERT: A  276 MET cc_start: 0.8705 (mmm) cc_final: 0.8392 (mmm)
REVERT: B  172 GLU cc_start: 0.6824 (tm-30) cc_final: 0.5739 (tm-30)
REVERT: B  209 ARG cc_start: 0.6700 (mtp-110) cc_final: 0.5379 (mmp80)
REVERT: B  245 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.8313 (p)
REVERT: B  271 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7893 (ptpt)
REVERT: B  282 ARG cc_start: 0.7750 (mtp-110) cc_final: 0.6886 (mtt180)
  outliers start: 12
  outliers final: 5
  residues processed: 102
  average time/residue: 1.4989
  time to fit residues: 159.6554
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  : 0.651 
-------------------------------------------------------------------------------
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  245 SER
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:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0970
   chunk 77 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0980
   chunk 26 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.4378

-------------------------------------------------------------------------------
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**
A 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.129576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.102540 restraints weight = 6858.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 1.41
r_work: 0.3053 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6898  Z= 0.184
  Angle     :  0.496   5.877   9360  Z= 0.247
  Chirality :  0.039   0.125   1100
  Planarity :  0.004   0.055   1176
  Dihedral  :  4.154  17.033    960
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 14.01 %
    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:  1.48 (0.28), residues: 896
  helix:  1.63 (0.20), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.22 (0.39), residues: 208

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   0.007   0.001   TYR B  94 
 ARG   0.002   0.000   ARG A  15 

*********************** 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: 10
    poor density    : 95
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6622 (ttm170) cc_final: 0.6126 (tpt170)
REVERT: A   17 ARG cc_start: 0.6190 (ttp80) cc_final: 0.5076 (tpt-90)
REVERT: A   20 GLN cc_start: 0.6770 (tm-30) cc_final: 0.5510 (tp40)
REVERT: A  276 MET cc_start: 0.8670 (mmm) cc_final: 0.8370 (mmm)
REVERT: B   61 GLN cc_start: 0.7746 (mt0) cc_final: 0.7504 (mt0)
REVERT: B  209 ARG cc_start: 0.6803 (mtp-110) cc_final: 0.5436 (mmp80)
REVERT: B  271 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7904 (ptpt)
REVERT: B  282 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.6928 (mtt180)
  outliers start: 10
  outliers final: 3
  residues processed: 102
  average time/residue: 1.5166
  time to fit residues: 161.4889
Evaluate side-chains
  90 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 8 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 56 optimal weight:    0.4980
   chunk 47 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 83 optimal weight:    0.3980
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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**
A 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.129344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.101667 restraints weight = 6771.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 1.43
r_work: 0.3032 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6898  Z= 0.207
  Angle     :  0.504   5.337   9360  Z= 0.250
  Chirality :  0.039   0.128   1100
  Planarity :  0.004   0.054   1176
  Dihedral  :  4.131  17.617    960
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 13.86 %
    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 (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:  1.81 (0.28), residues: 896
  helix:  1.87 (0.20), residues: 686
  sheet:  None (None), residues: 0
  loop : -1.06 (0.39), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 291 
 HIS   0.002   0.001   HIS B 234 
 PHE   0.030   0.001   PHE B 357 
 TYR   0.007   0.001   TYR B 255 
 ARG   0.002   0.000   ARG B  64 

*********************** 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  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6521 (ttm170) cc_final: 0.6315 (tpt170)
REVERT: A   20 GLN cc_start: 0.6735 (tm-30) cc_final: 0.5505 (tp40)
REVERT: A   30 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.6817 (ptpp)
REVERT: B   20 GLN cc_start: 0.5689 (mm110) cc_final: 0.5142 (tp40)
REVERT: B  209 ARG cc_start: 0.6807 (mtp-110) cc_final: 0.5390 (mmp80)
REVERT: B  271 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7861 (ptpt)
REVERT: B  282 ARG cc_start: 0.7731 (mtp-110) cc_final: 0.6887 (mtt180)
  outliers start: 12
  outliers final: 5
  residues processed: 99
  average time/residue: 1.5643
  time to fit residues: 161.5196
Evaluate side-chains
  94 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 63 optimal weight:    0.4980
   chunk 10 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 284 HIS
B 456 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.127808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.099863 restraints weight = 6716.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 1.42
r_work: 0.3009 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6898  Z= 0.253
  Angle     :  0.526   5.502   9360  Z= 0.261
  Chirality :  0.041   0.128   1100
  Planarity :  0.004   0.054   1176
  Dihedral  :  4.206  19.106    960
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 14.01 %
    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:  1.87 (0.28), residues: 896
  helix:  1.91 (0.19), residues: 686
  sheet:  None (None), residues: 0
  loop : -1.02 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 291 
 HIS   0.003   0.001   HIS B 234 
 PHE   0.029   0.002   PHE B 357 
 TYR   0.008   0.001   TYR A 210 
 ARG   0.002   0.000   ARG B  64 

*********************** 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
  109 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6686 (ttm170) cc_final: 0.6393 (tpt170)
REVERT: A   20 GLN cc_start: 0.6931 (tm-30) cc_final: 0.5650 (tp40)
REVERT: A   21 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.5939 (mm)
REVERT: A   30 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.6746 (ptpp)
REVERT: B   20 GLN cc_start: 0.5821 (mm110) cc_final: 0.5265 (tp40)
REVERT: B  209 ARG cc_start: 0.6874 (mtp-110) cc_final: 0.5456 (mmp80)
REVERT: B  271 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7939 (ptpt)
REVERT: B  282 ARG cc_start: 0.7799 (mtp-110) cc_final: 0.6929 (mtt180)
REVERT: B  456 GLN cc_start: 0.7410 (mt0) cc_final: 0.7185 (mt0)
  outliers start: 16
  outliers final: 6
  residues processed: 102
  average time/residue: 1.5948
  time to fit residues: 169.5894
Evaluate side-chains
  98 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 5 optimal weight:    0.1980
   chunk 48 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3487 r_free = 0.3487 target = 0.128146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.100304 restraints weight = 6688.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 1.42
r_work: 0.3009 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6898  Z= 0.225
  Angle     :  0.513   5.473   9360  Z= 0.255
  Chirality :  0.040   0.127   1100
  Planarity :  0.004   0.054   1176
  Dihedral  :  4.157  18.398    960
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 14.16 %
    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:  2.02 (0.27), residues: 896
  helix:  2.03 (0.19), residues: 686
  sheet:  None (None), residues: 0
  loop : -1.00 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 291 
 HIS   0.002   0.001   HIS B 234 
 PHE   0.029   0.001   PHE B 357 
 TYR   0.007   0.001   TYR A 210 
 ARG   0.002   0.000   ARG A  17 

*********************** 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
  109 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6676 (ttm170) cc_final: 0.6381 (tpt170)
REVERT: A   20 GLN cc_start: 0.6913 (tm-30) cc_final: 0.5626 (tp40)
REVERT: A   21 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.5901 (mm)
REVERT: B   20 GLN cc_start: 0.5778 (mm110) cc_final: 0.5239 (tp40)
REVERT: B  209 ARG cc_start: 0.6874 (mtp-110) cc_final: 0.5456 (mmp80)
REVERT: B  282 ARG cc_start: 0.7780 (mtp-110) cc_final: 0.6907 (mtt180)
  outliers start: 14
  outliers final: 5
  residues processed: 103
  average time/residue: 1.5093
  time to fit residues: 162.1838
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  : 0.724 
-------------------------------------------------------------------------------
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 80 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0980
   chunk 19 optimal weight:    0.8980
   chunk 75 optimal weight:    0.2980
   chunk 37 optimal weight:    0.9980
   chunk 47 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.4980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.128546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.101276 restraints weight = 6722.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 1.40
r_work: 0.3033 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6898  Z= 0.197
  Angle     :  0.501   5.782   9360  Z= 0.249
  Chirality :  0.039   0.125   1100
  Planarity :  0.004   0.053   1176
  Dihedral  :  4.078  17.004    960
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 14.60 %
    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 (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:  2.23 (0.28), residues: 896
  helix:  2.17 (0.19), residues: 686
  sheet:  None (None), residues: 0
  loop : -0.93 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 291 
 HIS   0.002   0.000   HIS B 234 
 PHE   0.033   0.001   PHE B 357 
 TYR   0.006   0.001   TYR B  94 
 ARG   0.002   0.000   ARG A  17 

*********************** 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
  108 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6603 (ttm170) cc_final: 0.6320 (tpt170)
REVERT: A   20 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.5539 (tp40)
REVERT: A   21 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.5833 (mm)
REVERT: A   91 MET cc_start: 0.8391 (mtt) cc_final: 0.8190 (mtt)
REVERT: A  457 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7179 (tp30)
REVERT: B   20 GLN cc_start: 0.5736 (mm110) cc_final: 0.5196 (tp40)
REVERT: B  209 ARG cc_start: 0.6843 (mtp-110) cc_final: 0.5420 (mmp80)
REVERT: B  282 ARG cc_start: 0.7771 (mtp-110) cc_final: 0.6885 (mtt180)
  outliers start: 13
  outliers final: 4
  residues processed: 104
  average time/residue: 1.5207
  time to fit residues: 164.9594
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  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 GLN
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  222 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 79 optimal weight:    0.5980
   chunk 56 optimal weight:    0.0570
   chunk 76 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 89 optimal weight:    2.9990
   chunk 34 optimal weight:    0.4980
   chunk 63 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
A 327 ASN

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 = 0.128860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.101587 restraints weight = 6736.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 1.41
r_work: 0.3037 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2906 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6898  Z= 0.193
  Angle     :  0.502   5.682   9360  Z= 0.249
  Chirality :  0.039   0.125   1100
  Planarity :  0.004   0.053   1176
  Dihedral  :  4.059  16.278    960
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 15.63 %
    Favored  : 83.19 %
  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:  2.32 (0.28), residues: 896
  helix:  2.22 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.90 (0.40), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 291 
 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   0.003   0.000   ARG A  17 

*********************** 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
  100 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6670 (ttm170) cc_final: 0.6399 (tpt170)
REVERT: A   20 GLN cc_start: 0.6872 (OUTLIER) cc_final: 0.5587 (tp40)
REVERT: A   21 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.5898 (mm)
REVERT: A  457 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7188 (tp30)
REVERT: B   20 GLN cc_start: 0.5773 (mm110) cc_final: 0.5221 (tp40)
REVERT: B  209 ARG cc_start: 0.6861 (mtp-110) cc_final: 0.5435 (mmp80)
REVERT: B  282 ARG cc_start: 0.7800 (mtp-110) cc_final: 0.6896 (mtt180)
  outliers start: 8
  outliers final: 4
  residues processed: 97
  average time/residue: 1.6099
  time to fit residues: 163.0654
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  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 GLN
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  222 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 10 optimal weight:    0.0270
   chunk 0 optimal weight:    7.9990
   chunk 68 optimal weight:    0.1980
   chunk 48 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
A 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.128697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.101710 restraints weight = 6803.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 1.38
r_work: 0.3037 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6898  Z= 0.203
  Angle     :  0.510   5.398   9360  Z= 0.252
  Chirality :  0.040   0.126   1100
  Planarity :  0.004   0.053   1176
  Dihedral  :  4.072  16.239    960
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 15.49 %
    Favored  : 83.33 %
  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:  2.36 (0.28), residues: 896
  helix:  2.25 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.88 (0.40), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 124 
 HIS   0.002   0.000   HIS B 234 
 PHE   0.035   0.001   PHE B 357 
 TYR   0.007   0.001   TYR A 210 
 ARG   0.003   0.000   ARG A  17 

********************** 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
  98 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.6738 (ttm170) cc_final: 0.6455 (tpt170)
REVERT: A   20 GLN cc_start: 0.6891 (tm-30) cc_final: 0.5621 (tp40)
REVERT: A   21 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.5936 (mm)
REVERT: A  167 ARG cc_start: 0.7102 (mpt180) cc_final: 0.6876 (mpt180)
REVERT: A  457 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7219 (tp30)
REVERT: B   20 GLN cc_start: 0.5826 (mm110) cc_final: 0.5264 (tp40)
REVERT: B  209 ARG cc_start: 0.6823 (mtp-110) cc_final: 0.5427 (mmp80)
REVERT: B  282 ARG cc_start: 0.7830 (mtp-110) cc_final: 0.6932 (mtt180)
  outliers start: 8
  outliers final: 4
  residues processed: 96
  average time/residue: 1.5919
  time to fit residues: 159.1101
Evaluate side-chains
  95 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
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  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:    0.5980
   chunk 87 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 56 optimal weight:    0.7980
   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 = 0.3483 r_free = 0.3483 target = 0.127883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.100007 restraints weight = 6721.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 1.42
r_work: 0.3012 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6898  Z= 0.246
  Angle     :  0.533   5.419   9360  Z= 0.264
  Chirality :  0.041   0.128   1100
  Planarity :  0.004   0.053   1176
  Dihedral  :  4.166  17.567    960
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 15.63 %
    Favored  : 83.04 %
  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:  2.22 (0.27), residues: 896
  helix:  2.18 (0.19), residues: 688
  sheet:  None (None), residues: 0
  loop : -1.01 (0.38), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 124 
 HIS   0.002   0.001   HIS B 234 
 PHE   0.035   0.002   PHE B 357 
 TYR   0.009   0.001   TYR A 210 
 ARG   0.003   0.000   ARG A  17 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4976.24 seconds
wall clock time: 85 minutes 40.39 seconds (5140.39 seconds total)