Starting phenix.real_space_refine
on Tue Feb 11 20:23:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rto_24685/02_2025/7rto_24685.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rto_24685/02_2025/7rto_24685.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rto_24685/02_2025/7rto_24685.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rto_24685/02_2025/7rto_24685.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rto_24685/02_2025/7rto_24685.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rto_24685/02_2025/7rto_24685.cif"
  }
  resolution = 3.8
  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=   0.009
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: 4
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    4160      2.51       5
     N    1205      2.21       5
     O    1228      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6607
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2006
          Classifications: {'peptide': 270}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 10, 'TRANS': 259}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 189
          Unresolved non-hydrogen angles: 229
          Unresolved non-hydrogen dihedrals: 164
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 92
    Chain: "B"
      Number of atoms: 2595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 348, 2595
          Classifications: {'peptide': 348}
          Incomplete info: {'truncation_to_alanine': 58}
          Link IDs: {'PTRANS': 10, 'TRANS': 337}
          Chain breaks: 4
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 216
          Unresolved non-hydrogen angles: 270
          Unresolved non-hydrogen dihedrals: 180
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 116
    Chain: "C"
      Number of atoms: 2006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2006
          Classifications: {'peptide': 270}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 10, 'TRANS': 259}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 189
          Unresolved non-hydrogen angles: 229
          Unresolved non-hydrogen dihedrals: 164
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 92
  Time building chain proxies: 4.08, per 1000 atoms: 0.62
  Number of scatterers: 6607
  At special positions: 0
  Unit cell: (104.72, 110.16, 114.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      14     16.00
     O    1228      8.00
     N    1205      7.00
     C    4160      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.50
  Conformation dependent library (CDL) restraints added in 821.4 milliseconds
  

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1664

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 6 sheets defined
      61.3% alpha, 11.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 64 through 80
      removed outlier: 3.716A  pdb=" N   SER A  68 " --> pdb=" O   SER A  64 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   SER A  80 " --> pdb=" O   ASN A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 135
      removed outlier: 3.558A  pdb=" N   ARG A  93 " --> pdb=" O   SER A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 340
      Proline residue:  A 326  - end of helix
    Processing helix  chain 'A' and resid 346 through 353
      removed outlier: 3.820A  pdb=" N   VAL A 350 " --> pdb=" O   ILE A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 438
    Processing helix  chain 'A' and resid 445 through 455
      removed outlier: 3.575A  pdb=" N   ARG A 449 " --> pdb=" O   MET A 445 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   THR A 455 " --> pdb=" O   VAL A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 483
    Processing helix  chain 'A' and resid 483 through 491
      removed outlier: 3.724A  pdb=" N   GLN A 487 " --> pdb=" O   ASP A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 509
    Processing helix  chain 'B' and resid 65 through 79
    Processing helix  chain 'B' and resid 89 through 115
      removed outlier: 4.241A  pdb=" N   TYR B 115 " --> pdb=" O   VAL B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 135
      removed outlier: 7.576A  pdb=" N   LYS B 125 " --> pdb=" O   GLU B 121 " (cutoff:3.500A)
      removed outlier: 7.484A  pdb=" N   GLU B 126 " --> pdb=" O   LYS B 122 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU B 127 " --> pdb=" O   PHE B 123 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   VAL B 130 " --> pdb=" O   GLU B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 177
    Processing helix  chain 'B' and resid 184 through 204
    Processing helix  chain 'B' and resid 249 through 256
      removed outlier: 3.902A  pdb=" N   GLU B 253 " --> pdb=" O   GLY B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 263
    Processing helix  chain 'B' and resid 296 through 330
      Proline residue:  B 326  - end of helix
    Processing helix  chain 'B' and resid 424 through 438
    Processing helix  chain 'B' and resid 445 through 454
    Processing helix  chain 'B' and resid 469 through 482
    Processing helix  chain 'B' and resid 483 through 491
      removed outlier: 3.572A  pdb=" N   GLN B 487 " --> pdb=" O   ASP B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 509
    Processing helix  chain 'B' and resid 510 through 513
    Processing helix  chain 'C' and resid 65 through 79
    Processing helix  chain 'C' and resid 89 through 135
      removed outlier: 4.531A  pdb=" N   ASN C 135 " --> pdb=" O   TYR C 131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 321 through 340
      Proline residue:  C 326  - end of helix
      removed outlier: 4.211A  pdb=" N   GLY C 340 " --> pdb=" O   LYS C 336 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 341 through 343
      No H-bonds generated for 'chain 'C' and resid 341 through 343'
    Processing helix  chain 'C' and resid 346 through 351
    Processing helix  chain 'C' and resid 424 through 438
      removed outlier: 3.524A  pdb=" N   SER C 438 " --> pdb=" O   ASN C 434 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 445 through 454
    Processing helix  chain 'C' and resid 469 through 483
    Processing helix  chain 'C' and resid 484 through 491
      removed outlier: 3.786A  pdb=" N   HIS C 489 " --> pdb=" O   GLU C 485 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 494 through 509
    Processing sheet with id=AA1, first strand: chain 'A' and resid 401 through 406
      removed outlier: 3.721A  pdb=" N   GLY A 462 " --> pdb=" O   VAL A 366 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   SER A 368 " --> pdb=" O   TYR A 460 " (cutoff:3.500A)
      removed outlier: 5.777A  pdb=" N   TYR A 460 " --> pdb=" O   SER A 368 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 410 through 414
    Processing sheet with id=AA3, first strand: chain 'B' and resid 401 through 408
      removed outlier: 3.884A  pdb=" N   GLY B 462 " --> pdb=" O   VAL B 366 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   SER B 368 " --> pdb=" O   TYR B 460 " (cutoff:3.500A)
      removed outlier: 5.617A  pdb=" N   TYR B 460 " --> pdb=" O   SER B 368 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 412 through 414
    Processing sheet with id=AA5, first strand: chain 'C' and resid 401 through 406
      removed outlier: 4.085A  pdb=" N   GLY C 462 " --> pdb=" O   VAL C 366 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   SER C 368 " --> pdb=" O   TYR C 460 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   TYR C 460 " --> pdb=" O   SER C 368 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 410 through 414

    468 hydrogen bonds defined for protein.
    1362 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: 1.89

  Time building geometry restraints manager: 1.76 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2122
        1.34 -     1.45: 955
        1.45 -     1.57: 3635
        1.57 -     1.69: 0
        1.69 -     1.81: 22
  Bond restraints: 6734
  Sorted by residual:
  bond pdb=" N   GLN A 360 "
       pdb=" CA  GLN A 360 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.034 1.33e-02 5.65e+03 6.65e+00
  bond pdb=" N   ASP A 406 "
       pdb=" CA  ASP A 406 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.31e-02 5.83e+03 6.35e+00
  bond pdb=" N   LEU C 113 "
       pdb=" CA  LEU C 113 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.19e-02 7.06e+03 5.52e+00
  bond pdb=" CG1 ILE C 490 "
       pdb=" CD1 ILE C 490 "
    ideal  model  delta    sigma   weight residual
    1.513  1.451  0.062 3.90e-02 6.57e+02 2.50e+00
  bond pdb=" CB  GLN C 361 "
       pdb=" CG  GLN C 361 "
    ideal  model  delta    sigma   weight residual
    1.520  1.478  0.042 3.00e-02 1.11e+03 1.94e+00
  ... (remaining 6729 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 8754
        1.90 -     3.79: 315
        3.79 -     5.69: 47
        5.69 -     7.59: 6
        7.59 -     9.48: 8
  Bond angle restraints: 9130
  Sorted by residual:
  angle pdb=" O   GLN A 360 "
        pdb=" C   GLN A 360 "
        pdb=" N   GLN A 361 "
      ideal   model   delta    sigma   weight residual
     122.18  125.88   -3.70 9.90e-01 1.02e+00 1.39e+01
  angle pdb=" CB  LYS A 511 "
        pdb=" CG  LYS A 511 "
        pdb=" CD  LYS A 511 "
      ideal   model   delta    sigma   weight residual
     111.30  119.34   -8.04 2.30e+00 1.89e-01 1.22e+01
  angle pdb=" CG1 ILE C 356 "
        pdb=" CB  ILE C 356 "
        pdb=" CG2 ILE C 356 "
      ideal   model   delta    sigma   weight residual
     110.70  101.37    9.33 3.00e+00 1.11e-01 9.68e+00
  angle pdb=" CA  GLN C 478 "
        pdb=" CB  GLN C 478 "
        pdb=" CG  GLN C 478 "
      ideal   model   delta    sigma   weight residual
     114.10  120.15   -6.05 2.00e+00 2.50e-01 9.16e+00
  angle pdb=" C   ALA C 359 "
        pdb=" N   GLN C 360 "
        pdb=" CA  GLN C 360 "
      ideal   model   delta    sigma   weight residual
     122.23  126.83   -4.60 1.57e+00 4.06e-01 8.59e+00
  ... (remaining 9125 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 3603
       17.85 -    35.69: 322
       35.69 -    53.53: 58
       53.53 -    71.38: 9
       71.38 -    89.22: 6
  Dihedral angle restraints: 3998
    sinusoidal: 1429
      harmonic: 2569
  Sorted by residual:
  dihedral pdb=" CA  TYR C  65 "
           pdb=" C   TYR C  65 "
           pdb=" N   GLY C  66 "
           pdb=" CA  GLY C  66 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.44  -22.56     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  HIS A 385 "
           pdb=" C   HIS A 385 "
           pdb=" N   HIS A 386 "
           pdb=" CA  HIS A 386 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.58   22.42     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  TYR B 404 "
           pdb=" C   TYR B 404 "
           pdb=" N   GLU B 405 "
           pdb=" CA  GLU B 405 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.48   20.52     0      5.00e+00 4.00e-02 1.68e+01
  ... (remaining 3995 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 955
       0.090 -    0.179: 61
       0.179 -    0.269: 8
       0.269 -    0.359: 0
       0.359 -    0.448: 1
  Chirality restraints: 1025
  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    2.20    0.45 2.00e-01 2.50e+01 5.02e+00
  chirality pdb=" CB  ILE C 356 "
            pdb=" CA  ILE C 356 "
            pdb=" CG1 ILE C 356 "
            pdb=" CG2 ILE C 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.89   -0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CA  ILE C 364 "
            pdb=" N   ILE C 364 "
            pdb=" C   ILE C 364 "
            pdb=" CB  ILE C 364 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.43e+00
  ... (remaining 1022 not shown)

  Planarity restraints: 1206
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 448 "    0.023 2.00e-02 2.50e+03   4.55e-02 2.07e+01
        pdb=" C   ARG A 448 "   -0.079 2.00e-02 2.50e+03
        pdb=" O   ARG A 448 "    0.029 2.00e-02 2.50e+03
        pdb=" N   ARG A 449 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR C 466 "   -0.013 2.00e-02 2.50e+03   2.64e-02 6.98e+00
        pdb=" C   TYR C 466 "    0.046 2.00e-02 2.50e+03
        pdb=" O   TYR C 466 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASP C 467 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 477 "   -0.012 2.00e-02 2.50e+03   2.36e-02 5.58e+00
        pdb=" C   ALA C 477 "    0.041 2.00e-02 2.50e+03
        pdb=" O   ALA C 477 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLN C 478 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1203 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 537
        2.74 -     3.28: 6560
        3.28 -     3.82: 10786
        3.82 -     4.36: 11393
        4.36 -     4.90: 20404
  Nonbonded interactions: 49680
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 493 "
            pdb=" NE2 GLN A 498 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" O   LEU A 450 "
            pdb=" OG  SER A 453 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" O   HIS A 384 "
            pdb=" ND1 HIS A 385 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" O   ALA A 369 "
            pdb=" OG  SER A 373 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" O   SER C  89 "
            pdb=" OG  SER C  89 "
     model   vdw
     2.385 3.040
  ... (remaining 49675 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.340
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.840
  Find NCS groups from input model:        0.110
  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:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   6734  Z= 0.243
  Angle     :  0.821   9.484   9130  Z= 0.449
  Chirality :  0.052   0.448   1025
  Planarity :  0.005   0.045   1206
  Dihedral  : 14.320  89.223   2334
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.00 %
    Favored  : 99.84 %
  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:  1.09 (0.30), residues: 870
  helix:  2.41 (0.23), residues: 490
  sheet: -0.19 (0.49), residues: 124
  loop : -2.30 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP C 371 
 HIS   0.010   0.001   HIS C 385 
 PHE   0.035   0.003   PHE C 470 
 TYR   0.027   0.002   TYR A 466 
 ARG   0.009   0.001   ARG A 474 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.759 
Fit side-chains
REVERT: A  360 GLN cc_start: 0.6902 (OUTLIER) cc_final: 0.6531 (tm-30)
REVERT: A  490 ILE cc_start: 0.8918 (mt) cc_final: 0.8640 (mt)
REVERT: B  108 ASN cc_start: 0.7412 (m110) cc_final: 0.7173 (m110)
REVERT: B  132 ASN cc_start: 0.5924 (t0) cc_final: 0.5670 (t0)
REVERT: C  448 ARG cc_start: 0.6949 (ttm-80) cc_final: 0.6679 (ttm-80)
  outliers start: 1
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1898
  time to fit residues: 34.3616
Evaluate side-chains
  94 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  360 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 66 optimal weight:    3.9990
   chunk 37 optimal weight:   20.0000
   chunk 22 optimal weight:    7.9990
   chunk 44 optimal weight:   40.0000
   chunk 35 optimal weight:   30.0000
   chunk 68 optimal weight:   50.0000
   chunk 26 optimal weight:   20.0000
   chunk 41 optimal weight:   20.0000
   chunk 51 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   overall best weight:    7.1992

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

Flipped N/Q/H residues before XYZ refinement:
A 365 HIS
A 478 GLN
B 177 GLN
** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.153940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.131657 restraints weight = 11664.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.131092 restraints weight = 13954.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.131950 restraints weight = 11318.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6734  Z= 0.283
  Angle     :  0.638   7.191   9130  Z= 0.346
  Chirality :  0.044   0.183   1025
  Planarity :  0.004   0.027   1206
  Dihedral  :  4.878  40.086    954
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 10.98 %
    Favored  : 87.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.21 (0.30), residues: 870
  helix:  2.25 (0.23), residues: 508
  sheet: -0.07 (0.47), residues: 137
  loop : -2.15 (0.39), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 411 
 HIS   0.009   0.001   HIS B 385 
 PHE   0.019   0.002   PHE B 378 
 TYR   0.028   0.002   TYR B 482 
 ARG   0.007   0.001   ARG A 474 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.750 
Fit side-chains
REVERT: A  488 MET cc_start: 0.7981 (tpp) cc_final: 0.7669 (tpp)
REVERT: A  490 ILE cc_start: 0.8938 (mt) cc_final: 0.8710 (mt)
REVERT: B  108 ASN cc_start: 0.7727 (m110) cc_final: 0.7431 (m-40)
REVERT: B  125 LYS cc_start: 0.3774 (mtpp) cc_final: 0.3260 (mtpp)
REVERT: B  132 ASN cc_start: 0.6374 (t0) cc_final: 0.5988 (t0)
REVERT: B  467 ASP cc_start: 0.6454 (m-30) cc_final: 0.5746 (p0)
REVERT: C  114 LYS cc_start: 0.2812 (tttp) cc_final: 0.2399 (tttm)
REVERT: C  427 GLU cc_start: 0.7810 (pt0) cc_final: 0.7580 (pt0)
  outliers start: 12
  outliers final: 10
  residues processed: 113
  average time/residue: 0.1670
  time to fit residues: 26.0125
Evaluate side-chains
  100 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  410 HIS
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain C residue  376 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 69 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 73 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9990
   chunk 38 optimal weight:    9.9990
   chunk 57 optimal weight:   10.0000
   chunk 70 optimal weight:    3.9990
   chunk 56 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 496 HIS
A 498 GLN
** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.154588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.131940 restraints weight = 11915.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.131169 restraints weight = 15230.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.132112 restraints weight = 12591.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.2159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6734  Z= 0.209
  Angle     :  0.573   6.205   9130  Z= 0.310
  Chirality :  0.042   0.165   1025
  Planarity :  0.003   0.024   1206
  Dihedral  :  4.381  18.659    951
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 14.59 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.32 (0.30), residues: 870
  helix:  2.45 (0.23), residues: 503
  sheet:  0.12 (0.49), residues: 128
  loop : -2.33 (0.37), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 411 
 HIS   0.009   0.001   HIS B 385 
 PHE   0.018   0.002   PHE B 378 
 TYR   0.020   0.002   TYR B 482 
 ARG   0.005   0.000   ARG A 474 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.733 
Fit side-chains
REVERT: A  360 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6776 (tm-30)
REVERT: A  445 MET cc_start: 0.8091 (tmm) cc_final: 0.7758 (tmm)
REVERT: A  488 MET cc_start: 0.8102 (tpp) cc_final: 0.7827 (tpp)
REVERT: B  108 ASN cc_start: 0.7695 (m110) cc_final: 0.7451 (m110)
REVERT: B  109 GLU cc_start: 0.5609 (tp30) cc_final: 0.5372 (tp30)
REVERT: B  132 ASN cc_start: 0.6147 (t0) cc_final: 0.5872 (t0)
REVERT: B  467 ASP cc_start: 0.6479 (m-30) cc_final: 0.5810 (p0)
REVERT: C  114 LYS cc_start: 0.2827 (tttp) cc_final: 0.2324 (tttm)
REVERT: C  118 LYS cc_start: 0.5260 (pttp) cc_final: 0.4324 (pttp)
  outliers start: 13
  outliers final: 10
  residues processed: 112
  average time/residue: 0.1690
  time to fit residues: 25.7767
Evaluate side-chains
  107 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain B residue  185 HIS
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  410 HIS
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain C residue  376 VAL
Chi-restraints excluded: chain C residue  424 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 3 optimal weight:    8.9990
   chunk 0 optimal weight:   40.0000
   chunk 84 optimal weight:    8.9990
   chunk 69 optimal weight:    7.9990
   chunk 74 optimal weight:    9.9990
   chunk 6 optimal weight:   50.0000
   chunk 23 optimal weight:    0.0170
   chunk 24 optimal weight:    3.9990
   chunk 43 optimal weight:   30.0000
   chunk 38 optimal weight:   10.0000
   overall best weight:    5.6026

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

Flipped N/Q/H residues before XYZ refinement:
** B 386 HIS ** 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 = 0.3830 r_free = 0.3830 target = 0.153948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.129480 restraints weight = 11939.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.126612 restraints weight = 11399.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.127536 restraints weight = 11281.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6734  Z= 0.231
  Angle     :  0.576   7.330   9130  Z= 0.312
  Chirality :  0.042   0.157   1025
  Planarity :  0.003   0.040   1206
  Dihedral  :  4.374  19.473    951
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 17.38 %
    Favored  : 80.33 %
  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:  1.30 (0.30), residues: 870
  helix:  2.34 (0.23), residues: 512
  sheet: -0.03 (0.47), residues: 137
  loop : -2.23 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 411 
 HIS   0.010   0.001   HIS B 385 
 PHE   0.019   0.002   PHE B 378 
 TYR   0.023   0.002   TYR B 482 
 ARG   0.006   0.000   ARG B 430 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.798 
Fit side-chains
REVERT: A  356 ILE cc_start: 0.8419 (mp) cc_final: 0.8043 (mp)
REVERT: A  360 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7232 (tm-30)
REVERT: A  488 MET cc_start: 0.8154 (tpp) cc_final: 0.7849 (tpp)
REVERT: B  108 ASN cc_start: 0.7706 (m110) cc_final: 0.7502 (m110)
REVERT: B  109 GLU cc_start: 0.5666 (tp30) cc_final: 0.5448 (tp30)
REVERT: B  132 ASN cc_start: 0.6351 (t0) cc_final: 0.5973 (t0)
REVERT: B  467 ASP cc_start: 0.6664 (m-30) cc_final: 0.6010 (p0)
REVERT: C  114 LYS cc_start: 0.2565 (tttp) cc_final: 0.2146 (tttm)
REVERT: C  118 LYS cc_start: 0.4909 (pttp) cc_final: 0.4143 (pttp)
REVERT: C  364 ILE cc_start: 0.9155 (mm) cc_final: 0.8812 (mm)
  outliers start: 14
  outliers final: 13
  residues processed: 106
  average time/residue: 0.1570
  time to fit residues: 23.4426
Evaluate side-chains
  104 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  410 HIS
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain C residue  376 VAL
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  496 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 81 optimal weight:   20.0000
   chunk 32 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 1 optimal weight:    8.9990
   chunk 59 optimal weight:    0.7980
   chunk 70 optimal weight:   50.0000
   chunk 43 optimal weight:   30.0000
   chunk 48 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 77 optimal weight:   20.0000
   chunk 28 optimal weight:    9.9990
   overall best weight:    5.7588

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

Flipped N/Q/H residues before XYZ refinement:
** B 386 HIS ** 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 = 0.3827 r_free = 0.3827 target = 0.153598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.131157 restraints weight = 11809.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.130479 restraints weight = 13555.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.131039 restraints weight = 11721.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6734  Z= 0.236
  Angle     :  0.577   6.630   9130  Z= 0.312
  Chirality :  0.042   0.161   1025
  Planarity :  0.003   0.027   1206
  Dihedral  :  4.377  19.192    951
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 17.87 %
    Favored  : 78.69 %
  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:  1.30 (0.30), residues: 870
  helix:  2.34 (0.23), residues: 514
  sheet: -0.11 (0.47), residues: 137
  loop : -2.21 (0.40), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 411 
 HIS   0.010   0.001   HIS B 385 
 PHE   0.018   0.002   PHE B 378 
 TYR   0.022   0.002   TYR B 482 
 ARG   0.005   0.000   ARG B 430 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.772 
Fit side-chains
REVERT: A  360 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7009 (tm-30)
REVERT: B  109 GLU cc_start: 0.5631 (tp30) cc_final: 0.5403 (tp30)
REVERT: B  132 ASN cc_start: 0.6064 (t0) cc_final: 0.5368 (t0)
REVERT: C  114 LYS cc_start: 0.2902 (tttp) cc_final: 0.2616 (tttm)
REVERT: C  118 LYS cc_start: 0.5039 (pttp) cc_final: 0.4260 (mmmt)
REVERT: C  364 ILE cc_start: 0.9128 (mm) cc_final: 0.8779 (mm)
  outliers start: 21
  outliers final: 17
  residues processed: 107
  average time/residue: 0.1556
  time to fit residues: 23.5709
Evaluate side-chains
  111 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  185 HIS
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  410 HIS
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain C residue  376 VAL
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  496 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 74 optimal weight:    5.9990
   chunk 67 optimal weight:    9.9990
   chunk 59 optimal weight:    0.6980
   chunk 36 optimal weight:   20.0000
   chunk 43 optimal weight:   30.0000
   chunk 44 optimal weight:   10.0000
   chunk 34 optimal weight:   50.0000
   chunk 84 optimal weight:   20.0000
   chunk 58 optimal weight:    5.9990
   chunk 10 optimal weight:   50.0000
   overall best weight:    6.5390

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

Flipped N/Q/H residues before XYZ refinement:
B 108 ASN
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.153102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.130040 restraints weight = 11785.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.127611 restraints weight = 14313.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.129241 restraints weight = 11388.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6734  Z= 0.256
  Angle     :  0.596   6.903   9130  Z= 0.320
  Chirality :  0.042   0.165   1025
  Planarity :  0.003   0.026   1206
  Dihedral  :  4.437  19.629    951
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 19.67 %
    Favored  : 76.72 %
  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:  1.24 (0.30), residues: 870
  helix:  2.31 (0.23), residues: 514
  sheet: -0.24 (0.46), residues: 137
  loop : -2.21 (0.40), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 411 
 HIS   0.010   0.001   HIS B 385 
 PHE   0.018   0.002   PHE B 378 
 TYR   0.024   0.002   TYR B 482 
 ARG   0.005   0.000   ARG B 430 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.757 
Fit side-chains
REVERT: A  360 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7026 (tm-30)
REVERT: A  427 GLU cc_start: 0.7328 (tm-30) cc_final: 0.7086 (tm-30)
REVERT: A  478 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8640 (mm-40)
REVERT: B  132 ASN cc_start: 0.6193 (t0) cc_final: 0.5382 (t0)
REVERT: C  114 LYS cc_start: 0.2676 (tttp) cc_final: 0.2452 (tttm)
REVERT: C  118 LYS cc_start: 0.4656 (pttp) cc_final: 0.4011 (mmmt)
REVERT: C  364 ILE cc_start: 0.9092 (mm) cc_final: 0.8718 (mm)
  outliers start: 22
  outliers final: 18
  residues processed: 108
  average time/residue: 0.1516
  time to fit residues: 23.3974
Evaluate side-chains
  106 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  410 HIS
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain C residue  376 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain C residue  496 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 44 optimal weight:   50.0000
   chunk 2 optimal weight:    0.0870
   chunk 18 optimal weight:    5.9990
   chunk 43 optimal weight:   40.0000
   chunk 55 optimal weight:    4.9990
   chunk 54 optimal weight:    8.9990
   chunk 65 optimal weight:   20.0000
   chunk 10 optimal weight:    0.9990
   chunk 69 optimal weight:   50.0000
   chunk 60 optimal weight:    9.9990
   chunk 71 optimal weight:    9.9990
   overall best weight:    4.2166

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

Flipped N/Q/H residues before XYZ refinement:
B 108 ASN
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.154439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.130309 restraints weight = 11684.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.128807 restraints weight = 9640.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.129729 restraints weight = 9257.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6734  Z= 0.195
  Angle     :  0.568   8.150   9130  Z= 0.304
  Chirality :  0.041   0.173   1025
  Planarity :  0.003   0.023   1206
  Dihedral  :  4.273  17.997    951
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.31 %
    Favored  : 75.41 %
  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:  1.40 (0.30), residues: 870
  helix:  2.46 (0.23), residues: 512
  sheet: -0.18 (0.46), residues: 137
  loop : -2.18 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 371 
 HIS   0.009   0.001   HIS B 385 
 PHE   0.017   0.002   PHE B 378 
 TYR   0.018   0.002   TYR A  65 
 ARG   0.004   0.000   ARG B 430 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.686 
Fit side-chains
REVERT: A  360 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.6863 (tm-30)
REVERT: A  478 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8591 (mm-40)
REVERT: B   84 ILE cc_start: 0.9459 (mm) cc_final: 0.9138 (tt)
REVERT: B  132 ASN cc_start: 0.6366 (t0) cc_final: 0.5483 (t0)
REVERT: C  118 LYS cc_start: 0.4506 (pttp) cc_final: 0.3929 (mmmt)
REVERT: C  364 ILE cc_start: 0.9097 (mm) cc_final: 0.8710 (mm)
  outliers start: 20
  outliers final: 17
  residues processed: 111
  average time/residue: 0.1511
  time to fit residues: 23.6015
Evaluate side-chains
  108 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  185 HIS
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  410 HIS
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain C residue  376 VAL
Chi-restraints excluded: chain C residue  419 THR
Chi-restraints excluded: chain C residue  427 GLU
Chi-restraints excluded: chain C residue  496 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 11 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 50 optimal weight:    9.9990
   chunk 55 optimal weight:    6.9990
   chunk 6 optimal weight:   40.0000
   chunk 4 optimal weight:    6.9990
   chunk 64 optimal weight:    6.9990
   chunk 29 optimal weight:    0.1980
   chunk 75 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   overall best weight:    5.4388

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

Flipped N/Q/H residues before XYZ refinement:
** B 386 HIS ** 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 = 0.3809 r_free = 0.3809 target = 0.152273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.130941 restraints weight = 11960.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.129940 restraints weight = 13110.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.130712 restraints weight = 11735.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.3050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6734  Z= 0.229
  Angle     :  0.598   8.895   9130  Z= 0.318
  Chirality :  0.042   0.175   1025
  Planarity :  0.003   0.023   1206
  Dihedral  :  4.346  18.685    951
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 22.46 %
    Favored  : 74.26 %
  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:  1.30 (0.30), residues: 870
  helix:  2.41 (0.22), residues: 512
  sheet: -0.31 (0.46), residues: 139
  loop : -2.21 (0.40), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 371 
 HIS   0.010   0.001   HIS B 385 
 PHE   0.018   0.002   PHE B 378 
 TYR   0.022   0.002   TYR B 482 
 ARG   0.004   0.000   ARG B 430 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.797 
Fit side-chains
REVERT: A  360 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.6835 (tm-30)
REVERT: A  478 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8587 (mm-40)
REVERT: B   84 ILE cc_start: 0.9445 (mm) cc_final: 0.9127 (tt)
REVERT: B  132 ASN cc_start: 0.6334 (t0) cc_final: 0.5533 (t0)
REVERT: C  118 LYS cc_start: 0.5021 (pttp) cc_final: 0.4320 (mmmt)
REVERT: C  364 ILE cc_start: 0.9086 (mm) cc_final: 0.8693 (mm)
  outliers start: 20
  outliers final: 17
  residues processed: 100
  average time/residue: 0.1521
  time to fit residues: 21.7601
Evaluate side-chains
  104 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  410 HIS
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain C residue  376 VAL
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  427 GLU
Chi-restraints excluded: chain C residue  451 VAL
Chi-restraints excluded: chain C residue  496 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 50 optimal weight:    8.9990
   chunk 39 optimal weight:    7.9990
   chunk 56 optimal weight:    7.9990
   chunk 43 optimal weight:   20.0000
   chunk 28 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 6 optimal weight:   50.0000
   chunk 72 optimal weight:   10.0000
   chunk 66 optimal weight:    9.9990
   chunk 87 optimal weight:    5.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 108 ASN
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.152309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.130741 restraints weight = 11941.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.129382 restraints weight = 14323.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.130788 restraints weight = 11056.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.3161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6734  Z= 0.242
  Angle     :  0.612   9.046   9130  Z= 0.326
  Chirality :  0.042   0.195   1025
  Planarity :  0.003   0.024   1206
  Dihedral  :  4.418  18.759    951
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 22.46 %
    Favored  : 74.26 %
  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:  1.16 (0.29), residues: 870
  helix:  2.29 (0.22), residues: 512
  sheet: -0.37 (0.46), residues: 139
  loop : -2.27 (0.39), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 371 
 HIS   0.010   0.001   HIS B 385 
 PHE   0.018   0.002   PHE B 378 
 TYR   0.023   0.002   TYR B 482 
 ARG   0.004   0.000   ARG B 430 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A  356 ILE cc_start: 0.8017 (mp) cc_final: 0.7449 (mm)
REVERT: A  360 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6926 (tm-30)
REVERT: A  410 HIS cc_start: 0.7699 (m-70) cc_final: 0.7493 (m-70)
REVERT: A  478 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8235 (mm-40)
REVERT: B   84 ILE cc_start: 0.9428 (mm) cc_final: 0.9095 (tt)
REVERT: B  132 ASN cc_start: 0.6379 (t0) cc_final: 0.5550 (t0)
REVERT: C  118 LYS cc_start: 0.4924 (pttp) cc_final: 0.4252 (mmmt)
REVERT: C  364 ILE cc_start: 0.9096 (mm) cc_final: 0.8698 (mm)
  outliers start: 20
  outliers final: 17
  residues processed: 102
  average time/residue: 0.1578
  time to fit residues: 22.5365
Evaluate side-chains
  104 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  410 HIS
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain C residue   95 ILE
Chi-restraints excluded: chain C residue  376 VAL
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  427 GLU
Chi-restraints excluded: chain C residue  496 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 77 optimal weight:   30.0000
   chunk 46 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 55 optimal weight:    8.9990
   chunk 58 optimal weight:    7.9990
   chunk 20 optimal weight:   10.0000
   chunk 40 optimal weight:   40.0000
   chunk 3 optimal weight:   10.0000
   chunk 45 optimal weight:   40.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 489 HIS
** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.153401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.132184 restraints weight = 12026.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.131168 restraints weight = 14487.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.132873 restraints weight = 11329.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6734  Z= 0.223
  Angle     :  0.612   9.896   9130  Z= 0.325
  Chirality :  0.042   0.194   1025
  Planarity :  0.003   0.024   1206
  Dihedral  :  4.326  18.184    951
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 22.46 %
    Favored  : 74.26 %
  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:  1.23 (0.30), residues: 870
  helix:  2.34 (0.23), residues: 511
  sheet: -0.35 (0.46), residues: 139
  loop : -2.19 (0.40), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 411 
 HIS   0.009   0.001   HIS B 385 
 PHE   0.018   0.002   PHE B 378 
 TYR   0.020   0.002   TYR B 482 
 ARG   0.004   0.000   ARG B 430 

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

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

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1740 Ramachandran restraints generated.
    870 Oldfield, 0 Emsley, 870 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A  356 ILE cc_start: 0.7912 (mp) cc_final: 0.7334 (mm)
REVERT: A  360 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6837 (tm-30)
REVERT: A  478 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8584 (mm-40)
REVERT: B  132 ASN cc_start: 0.6377 (t0) cc_final: 0.5540 (t0)
REVERT: C  118 LYS cc_start: 0.4922 (pttp) cc_final: 0.4252 (mmmt)
REVERT: C  364 ILE cc_start: 0.9058 (mm) cc_final: 0.8670 (mm)
  outliers start: 20
  outliers final: 16
  residues processed: 99
  average time/residue: 0.1602
  time to fit residues: 22.2907
Evaluate side-chains
  101 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  104 ASP
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  478 GLN
Chi-restraints excluded: chain B residue  106 GLN
Chi-restraints excluded: chain B residue  376 VAL
Chi-restraints excluded: chain B residue  390 SER
Chi-restraints excluded: chain B residue  407 LEU
Chi-restraints excluded: chain B residue  410 HIS
Chi-restraints excluded: chain B residue  424 THR
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain C residue   95 ILE
Chi-restraints excluded: chain C residue  376 VAL
Chi-restraints excluded: chain C residue  389 GLU
Chi-restraints excluded: chain C residue  424 THR
Chi-restraints excluded: chain C residue  496 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 37 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9980
   chunk 78 optimal weight:    6.9990
   chunk 71 optimal weight:   30.0000
   chunk 35 optimal weight:   10.0000
   chunk 69 optimal weight:   20.0000
   chunk 81 optimal weight:   20.0000
   chunk 12 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 52 optimal weight:    8.9990
   chunk 45 optimal weight:   50.0000
   overall best weight:    4.7986

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

Flipped N/Q/H residues before XYZ refinement:
** B 386 HIS ** 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 = 0.3831 r_free = 0.3831 target = 0.153939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.132246 restraints weight = 11859.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.131990 restraints weight = 13526.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.132400 restraints weight = 10230.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.3274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6734  Z= 0.213
  Angle     :  0.602   9.968   9130  Z= 0.321
  Chirality :  0.042   0.182   1025
  Planarity :  0.003   0.023   1206
  Dihedral  :  4.314  18.085    951
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 22.30 %
    Favored  : 74.59 %
  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:  1.25 (0.30), residues: 870
  helix:  2.35 (0.23), residues: 511
  sheet: -0.36 (0.46), residues: 139
  loop : -2.16 (0.40), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 371 
 HIS   0.010   0.001   HIS B 385 
 PHE   0.018   0.002   PHE B 378 
 TYR   0.020   0.002   TYR B 482 
 ARG   0.003   0.000   ARG B 430 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1844.84 seconds
wall clock time: 34 minutes 23.90 seconds (2063.90 seconds total)