Starting phenix.real_space_refine
on Thu Jan 16 23:29:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xw2_38728/01_2025/8xw2_38728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xw2_38728/01_2025/8xw2_38728.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xw2_38728/01_2025/8xw2_38728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xw2_38728/01_2025/8xw2_38728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xw2_38728/01_2025/8xw2_38728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xw2_38728/01_2025/8xw2_38728.cif"
  }
  resolution = 3.59
  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=   0.004 sd=   0.066
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      48      5.16       5
     C    6744      2.51       5
     N    1650      2.21       5
     O    1708      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 68 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 10150
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 634, 5075
          Classifications: {'peptide': 634}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 34, 'TRANS': 599}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 39
  Restraints were copied for chains:
    B
  Time building chain proxies: 9.72, per 1000 atoms: 0.96
  Number of scatterers: 10150
  At special positions: 0
  Unit cell: (91.785, 140.315, 98.115, 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      48     16.00
     O    1708      8.00
     N    1650      7.00
     C    6744      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: 2.88
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2432

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 2 sheets defined
      77.1% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 30
      removed outlier: 3.501A  pdb=" N   LEU A  30 " --> pdb=" O   ALA A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 33
      No H-bonds generated for 'chain 'A' and resid 31 through 33'
    Processing helix  chain 'A' and resid 34 through 39
    Processing helix  chain 'A' and resid 74 through 80
      removed outlier: 3.757A  pdb=" N   LEU A  80 " --> pdb=" O   MET A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 92
    Processing helix  chain 'A' and resid 92 through 121
      removed outlier: 4.119A  pdb=" N   TYR A 102 " --> pdb=" O   TYR A  98 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   TRP A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      Proline residue:  A 111  - end of helix
    Processing helix  chain 'A' and resid 157 through 195
    Processing helix  chain 'A' and resid 198 through 201
    Processing helix  chain 'A' and resid 216 through 229
    Processing helix  chain 'A' and resid 242 through 269
    Processing helix  chain 'A' and resid 290 through 313
    Processing helix  chain 'A' and resid 315 through 317
      No H-bonds generated for 'chain 'A' and resid 315 through 317'
    Processing helix  chain 'A' and resid 329 through 338
    Processing helix  chain 'A' and resid 360 through 366
      removed outlier: 3.747A  pdb=" N   ALA A 365 " --> pdb=" O   SER A 362 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ILE A 366 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 370 through 389
    Processing helix  chain 'A' and resid 389 through 400
      removed outlier: 3.786A  pdb=" N   ILE A 393 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 438
      Proline residue:  A 430  - end of helix
    Processing helix  chain 'A' and resid 440 through 452
    Processing helix  chain 'A' and resid 456 through 475
    Processing helix  chain 'A' and resid 477 through 489
    Processing helix  chain 'A' and resid 504 through 509
    Processing helix  chain 'A' and resid 512 through 534
      removed outlier: 3.615A  pdb=" N   ALA A 526 " --> pdb=" O   VAL A 522 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   GLY A 527 " --> pdb=" O   ASP A 523 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   MET A 534 " --> pdb=" O   GLY A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 548
    Processing helix  chain 'A' and resid 554 through 559
    Processing helix  chain 'A' and resid 565 through 584
      Proline residue:  A 571  - end of helix
    Processing helix  chain 'A' and resid 587 through 589
      No H-bonds generated for 'chain 'A' and resid 587 through 589'
    Processing helix  chain 'A' and resid 590 through 612
      removed outlier: 3.724A  pdb=" N   ILE A 594 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 646
    Processing helix  chain 'A' and resid 647 through 649
      No H-bonds generated for 'chain 'A' and resid 647 through 649'
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 659 through 677
      removed outlier: 4.024A  pdb=" N   VAL A 663 " --> pdb=" O   ILE A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 682
    Processing helix  chain 'A' and resid 684 through 699
    Processing helix  chain 'A' and resid 703 through 710
      removed outlier: 4.109A  pdb=" N   ASN A 710 " --> pdb=" O   GLY A 706 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 30
      removed outlier: 3.501A  pdb=" N   LEU B  30 " --> pdb=" O   ALA B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 33
      No H-bonds generated for 'chain 'B' and resid 31 through 33'
    Processing helix  chain 'B' and resid 34 through 39
    Processing helix  chain 'B' and resid 74 through 80
      removed outlier: 3.756A  pdb=" N   LEU B  80 " --> pdb=" O   MET B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 92
    Processing helix  chain 'B' and resid 92 through 121
      removed outlier: 4.118A  pdb=" N   TYR B 102 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   TRP B 103 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
    Processing helix  chain 'B' and resid 157 through 195
    Processing helix  chain 'B' and resid 198 through 201
    Processing helix  chain 'B' and resid 216 through 229
    Processing helix  chain 'B' and resid 242 through 269
    Processing helix  chain 'B' and resid 290 through 313
    Processing helix  chain 'B' and resid 315 through 317
      No H-bonds generated for 'chain 'B' and resid 315 through 317'
    Processing helix  chain 'B' and resid 329 through 338
    Processing helix  chain 'B' and resid 360 through 366
      removed outlier: 3.746A  pdb=" N   ALA B 365 " --> pdb=" O   SER B 362 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ILE B 366 " --> pdb=" O   ASN B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 369
      No H-bonds generated for 'chain 'B' and resid 367 through 369'
    Processing helix  chain 'B' and resid 370 through 389
    Processing helix  chain 'B' and resid 389 through 400
      removed outlier: 3.786A  pdb=" N   ILE B 393 " --> pdb=" O   PHE B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 438
      Proline residue:  B 430  - end of helix
    Processing helix  chain 'B' and resid 440 through 452
    Processing helix  chain 'B' and resid 456 through 475
    Processing helix  chain 'B' and resid 477 through 489
    Processing helix  chain 'B' and resid 504 through 509
    Processing helix  chain 'B' and resid 512 through 534
      removed outlier: 3.617A  pdb=" N   ALA B 526 " --> pdb=" O   VAL B 522 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   GLY B 527 " --> pdb=" O   ASP B 523 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU B 533 " --> pdb=" O   ALA B 529 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   MET B 534 " --> pdb=" O   GLY B 530 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 534 through 548
    Processing helix  chain 'B' and resid 554 through 559
    Processing helix  chain 'B' and resid 565 through 584
      Proline residue:  B 571  - end of helix
    Processing helix  chain 'B' and resid 587 through 589
      No H-bonds generated for 'chain 'B' and resid 587 through 589'
    Processing helix  chain 'B' and resid 590 through 612
      removed outlier: 3.724A  pdb=" N   ILE B 594 " --> pdb=" O   LEU B 590 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 623 through 646
    Processing helix  chain 'B' and resid 647 through 649
      No H-bonds generated for 'chain 'B' and resid 647 through 649'
    Processing helix  chain 'B' and resid 654 through 659
    Processing helix  chain 'B' and resid 659 through 677
      removed outlier: 4.024A  pdb=" N   VAL B 663 " --> pdb=" O   ILE B 659 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 677 through 682
    Processing helix  chain 'B' and resid 684 through 699
    Processing helix  chain 'B' and resid 703 through 710
      removed outlier: 4.108A  pdb=" N   ASN B 710 " --> pdb=" O   GLY B 706 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 240
      removed outlier: 5.660A  pdb=" N   ALA A 322 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 240
      removed outlier: 5.660A  pdb=" N   ALA B 322 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)

    691 hydrogen bonds defined for protein.
    2049 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: 2.89

  Time building geometry restraints manager: 3.26 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: 3094
        1.34 -     1.46: 2463
        1.46 -     1.58: 4795
        1.58 -     1.70: 0
        1.70 -     1.82: 88
  Bond restraints: 10440
  Sorted by residual:
  bond pdb=" CG  LEU A 441 "
       pdb=" CD2 LEU A 441 "
    ideal  model  delta    sigma   weight residual
    1.521  1.459  0.062 3.30e-02 9.18e+02 3.58e+00
  bond pdb=" CG  LEU B 441 "
       pdb=" CD2 LEU B 441 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.46e+00
  bond pdb=" C   ASN A 344 "
       pdb=" N   PRO A 345 "
    ideal  model  delta    sigma   weight residual
    1.334  1.319  0.014 8.40e-03 1.42e+04 2.95e+00
  bond pdb=" C   ASN B 344 "
       pdb=" N   PRO B 345 "
    ideal  model  delta    sigma   weight residual
    1.334  1.319  0.014 8.40e-03 1.42e+04 2.89e+00
  bond pdb=" CD  GLU B 297 "
       pdb=" OE1 GLU B 297 "
    ideal  model  delta    sigma   weight residual
    1.249  1.222  0.027 1.90e-02 2.77e+03 2.06e+00
  ... (remaining 10435 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 13606
        1.59 -     3.18: 455
        3.18 -     4.77: 95
        4.77 -     6.36: 30
        6.36 -     7.95: 14
  Bond angle restraints: 14200
  Sorted by residual:
  angle pdb=" C   ALA B 296 "
        pdb=" N   GLU B 297 "
        pdb=" CA  GLU B 297 "
      ideal   model   delta    sigma   weight residual
     121.14  113.19    7.95 1.75e+00 3.27e-01 2.07e+01
  angle pdb=" C   ALA A 296 "
        pdb=" N   GLU A 297 "
        pdb=" CA  GLU A 297 "
      ideal   model   delta    sigma   weight residual
     121.14  113.20    7.94 1.75e+00 3.27e-01 2.06e+01
  angle pdb=" N   GLU A 297 "
        pdb=" CA  GLU A 297 "
        pdb=" CB  GLU A 297 "
      ideal   model   delta    sigma   weight residual
     110.40  115.85   -5.45 1.63e+00 3.76e-01 1.12e+01
  angle pdb=" N   GLU B 297 "
        pdb=" CA  GLU B 297 "
        pdb=" CB  GLU B 297 "
      ideal   model   delta    sigma   weight residual
     110.40  115.84   -5.44 1.63e+00 3.76e-01 1.12e+01
  angle pdb=" N   PRO B 345 "
        pdb=" CA  PRO B 345 "
        pdb=" C   PRO B 345 "
      ideal   model   delta    sigma   weight residual
     114.68  111.35    3.33 1.04e+00 9.25e-01 1.03e+01
  ... (remaining 14195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 5597
       17.96 -    35.92: 426
       35.92 -    53.87: 83
       53.87 -    71.83: 12
       71.83 -    89.79: 10
  Dihedral angle restraints: 6128
    sinusoidal: 2386
      harmonic: 3742
  Sorted by residual:
  dihedral pdb=" CA  ILE A 108 "
           pdb=" C   ILE A 108 "
           pdb=" N   PHE A 109 "
           pdb=" CA  PHE A 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.30  -19.70     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  ILE B 108 "
           pdb=" C   ILE B 108 "
           pdb=" N   PHE B 109 "
           pdb=" CA  PHE B 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.30  -19.70     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  ASN B 475 "
           pdb=" C   ASN B 475 "
           pdb=" N   VAL B 476 "
           pdb=" CA  VAL B 476 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.44  -17.56     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 6125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 1491
       0.088 -    0.176: 109
       0.176 -    0.264: 2
       0.264 -    0.351: 0
       0.351 -    0.439: 2
  Chirality restraints: 1604
  Sorted by residual:
  chirality pdb=" CB  ILE A 112 "
            pdb=" CA  ILE A 112 "
            pdb=" CG1 ILE A 112 "
            pdb=" CG2 ILE A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.21    0.44 2.00e-01 2.50e+01 4.82e+00
  chirality pdb=" CB  ILE B 112 "
            pdb=" CA  ILE B 112 "
            pdb=" CG1 ILE B 112 "
            pdb=" CG2 ILE B 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.21    0.44 2.00e-01 2.50e+01 4.77e+00
  chirality pdb=" CA  GLU A 297 "
            pdb=" N   GLU A 297 "
            pdb=" C   GLU A 297 "
            pdb=" CB  GLU A 297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.90e-01
  ... (remaining 1601 not shown)

  Planarity restraints: 1762
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 391 "   -0.045 5.00e-02 4.00e+02   6.70e-02 7.19e+00
        pdb=" N   PRO B 392 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO B 392 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 392 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 391 "    0.045 5.00e-02 4.00e+02   6.69e-02 7.16e+00
        pdb=" N   PRO A 392 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 392 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 392 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 677 "    0.036 5.00e-02 4.00e+02   5.47e-02 4.78e+00
        pdb=" N   PRO B 678 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO B 678 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 678 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1759 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 379
        2.71 -     3.26: 10994
        3.26 -     3.81: 17007
        3.81 -     4.35: 19419
        4.35 -     4.90: 33328
  Nonbonded interactions: 81127
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 354 "
            pdb=" OH  TYR A 712 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" O   PRO B 354 "
            pdb=" OH  TYR B 712 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" OG  SER A 216 "
            pdb=" OE1 GLU A 219 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OG  SER B 216 "
            pdb=" OE1 GLU B 219 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" NE  ARG A 343 "
            pdb=" OE2 GLU B 687 "
     model   vdw
     2.236 3.120
  ... (remaining 81122 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: 0.05
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 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:             0.850
  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:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     28.710
  Find NCS groups from input model:        0.160
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
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   0.062  10440  Z= 0.304
  Angle     :  0.756   7.955  14200  Z= 0.418
  Chirality :  0.047   0.439   1604
  Planarity :  0.005   0.067   1762
  Dihedral  : 13.677  89.790   3696
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  0.69 (0.24), residues: 1248
  helix:  1.62 (0.18), residues: 866
  sheet: -1.63 (0.86), residues: 34
  loop : -2.42 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 624 
 HIS   0.005   0.001   HIS B 542 
 PHE   0.023   0.002   PHE A 471 
 TYR   0.025   0.002   TYR A 294 
 ARG   0.004   0.001   ARG A  36 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 1.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 SER cc_start: 0.8340 (p) cc_final: 0.8039 (m)
REVERT: A   74 ASN cc_start: 0.8548 (p0) cc_final: 0.7948 (p0)
REVERT: A  165 MET cc_start: 0.8227 (tpt) cc_final: 0.7867 (tpp)
REVERT: A  167 TYR cc_start: 0.7771 (m-80) cc_final: 0.7267 (m-10)
REVERT: A  256 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8031 (tm-30)
REVERT: A  440 PHE cc_start: 0.7389 (m-80) cc_final: 0.7174 (m-80)
REVERT: B   40 SER cc_start: 0.8420 (p) cc_final: 0.8163 (m)
REVERT: B  165 MET cc_start: 0.8360 (tpt) cc_final: 0.7896 (tpp)
REVERT: B  256 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7835 (tm-30)
REVERT: B  437 PHE cc_start: 0.8638 (m-80) cc_final: 0.8428 (m-10)
REVERT: B  615 GLN cc_start: 0.6946 (mt0) cc_final: 0.6601 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 225
  average time/residue: 0.1754
  time to fit residues: 59.5770
Evaluate side-chains
  173 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    0.8980
   chunk 95 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 98 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0060
   chunk 114 optimal weight:    0.5980
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 GLN
A 472 ASN
A 639 GLN
B 338 GLN
B 639 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.137111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.103445 restraints weight = 17271.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.106400 restraints weight = 9741.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.108250 restraints weight = 6955.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10440  Z= 0.209
  Angle     :  0.655  12.984  14200  Z= 0.324
  Chirality :  0.043   0.153   1604
  Planarity :  0.005   0.056   1762
  Dihedral  :  4.409  19.202   1360
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  8.88 %
    Favored  : 89.98 %
  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:  0.70 (0.24), residues: 1248
  helix:  1.79 (0.17), residues: 856
  sheet: -1.82 (0.73), residues: 46
  loop : -2.74 (0.29), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 624 
 HIS   0.004   0.001   HIS A 293 
 PHE   0.024   0.002   PHE A 428 
 TYR   0.013   0.001   TYR A 468 
 ARG   0.002   0.000   ARG B  36 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 195
  time to evaluate  : 1.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 SER cc_start: 0.8120 (p) cc_final: 0.7698 (m)
REVERT: A   74 ASN cc_start: 0.8460 (p0) cc_final: 0.7841 (p0)
REVERT: A  102 TYR cc_start: 0.8669 (m-10) cc_final: 0.8434 (m-80)
REVERT: A  165 MET cc_start: 0.8055 (tpt) cc_final: 0.7661 (ttt)
REVERT: A  256 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8195 (tm-30)
REVERT: A  559 MET cc_start: 0.8286 (tpt) cc_final: 0.7637 (tpt)
REVERT: A  643 MET cc_start: 0.7865 (tmm) cc_final: 0.7497 (tmm)
REVERT: B   40 SER cc_start: 0.8172 (p) cc_final: 0.7927 (m)
REVERT: B  256 GLN cc_start: 0.8354 (tm-30) cc_final: 0.8010 (tm-30)
REVERT: B  643 MET cc_start: 0.8063 (tmm) cc_final: 0.7863 (tmm)
  outliers start: 12
  outliers final: 7
  residues processed: 201
  average time/residue: 0.1778
  time to fit residues: 53.9603
Evaluate side-chains
  175 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 168
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  578 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 85 optimal weight:   30.0000
   chunk 22 optimal weight:   30.0000
   chunk 65 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A 243 ASN ** 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 = 0.3709 r_free = 0.3709 target = 0.136517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.102547 restraints weight = 17534.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.105536 restraints weight = 9822.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.107405 restraints weight = 6979.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10440  Z= 0.213
  Angle     :  0.626  13.346  14200  Z= 0.310
  Chirality :  0.043   0.152   1604
  Planarity :  0.005   0.056   1762
  Dihedral  :  4.241  18.848   1360
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 12.00 %
    Favored  : 86.20 %
  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:  0.85 (0.24), residues: 1248
  helix:  1.94 (0.18), residues: 846
  sheet: -2.19 (0.72), residues: 46
  loop : -2.58 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 624 
 HIS   0.003   0.001   HIS B 628 
 PHE   0.026   0.001   PHE A 159 
 TYR   0.013   0.001   TYR A 468 
 ARG   0.002   0.000   ARG B 374 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 187
  time to evaluate  : 1.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 SER cc_start: 0.8192 (p) cc_final: 0.7807 (m)
REVERT: A   74 ASN cc_start: 0.8468 (p0) cc_final: 0.7883 (p0)
REVERT: A  256 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8217 (tm-30)
REVERT: A  559 MET cc_start: 0.8282 (tpt) cc_final: 0.7897 (tpt)
REVERT: B  165 MET cc_start: 0.7987 (tpp) cc_final: 0.7612 (tpp)
REVERT: B  256 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7999 (tm-30)
REVERT: B  559 MET cc_start: 0.8277 (tpp) cc_final: 0.6918 (ppp)
  outliers start: 19
  outliers final: 14
  residues processed: 199
  average time/residue: 0.1797
  time to fit residues: 54.6479
Evaluate side-chains
  192 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 178
  time to evaluate  : 1.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  261 TYR
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  665 THR
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  472 ASN
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  578 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 118 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 44 optimal weight:    0.2980
   chunk 92 optimal weight:    4.9990
   chunk 23 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 15 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.3739 r_free = 0.3739 target = 0.138751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.105120 restraints weight = 17292.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.108093 restraints weight = 9736.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.109955 restraints weight = 6923.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10440  Z= 0.169
  Angle     :  0.618  13.632  14200  Z= 0.304
  Chirality :  0.042   0.151   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  4.123  19.597   1360
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 13.23 %
    Favored  : 84.97 %
  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:  0.96 (0.24), residues: 1248
  helix:  1.88 (0.18), residues: 868
  sheet: -2.29 (0.71), residues: 46
  loop : -2.39 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 624 
 HIS   0.002   0.000   HIS A 293 
 PHE   0.027   0.001   PHE B 159 
 TYR   0.010   0.001   TYR A 468 
 ARG   0.002   0.000   ARG B 309 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 191
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 SER cc_start: 0.8162 (p) cc_final: 0.7784 (m)
REVERT: A   74 ASN cc_start: 0.8427 (p0) cc_final: 0.7880 (p0)
REVERT: A  165 MET cc_start: 0.8280 (tpp) cc_final: 0.8055 (tpp)
REVERT: A  256 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8244 (tm-30)
REVERT: A  311 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8012 (pt0)
REVERT: A  523 ASP cc_start: 0.7969 (t70) cc_final: 0.7629 (t70)
REVERT: A  559 MET cc_start: 0.8184 (tpt) cc_final: 0.7965 (tpt)
REVERT: B  165 MET cc_start: 0.8444 (tpp) cc_final: 0.8191 (tpp)
REVERT: B  256 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8047 (tm-30)
REVERT: B  389 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.6583 (t80)
REVERT: B  661 LEU cc_start: 0.8211 (tp) cc_final: 0.8004 (tp)
  outliers start: 19
  outliers final: 11
  residues processed: 198
  average time/residue: 0.1777
  time to fit residues: 53.6657
Evaluate side-chains
  186 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 173
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  646 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 111 optimal weight:    0.3980
   chunk 32 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   chunk 35 optimal weight:    6.9990
   chunk 43 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 81 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 93 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 639 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.138503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.104655 restraints weight = 17153.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.107573 restraints weight = 9788.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.109425 restraints weight = 7006.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10440  Z= 0.190
  Angle     :  0.625  14.936  14200  Z= 0.304
  Chirality :  0.042   0.164   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  4.064  19.614   1360
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.84 %
    Favored  : 83.55 %
  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:  1.12 (0.25), residues: 1248
  helix:  1.95 (0.18), residues: 872
  sheet: -2.48 (0.77), residues: 36
  loop : -2.22 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 624 
 HIS   0.002   0.000   HIS B 628 
 PHE   0.026   0.001   PHE B 428 
 TYR   0.010   0.001   TYR A 468 
 ARG   0.002   0.000   ARG B 374 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 191
  time to evaluate  : 1.029 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.8432 (p0) cc_final: 0.7921 (p0)
REVERT: A  165 MET cc_start: 0.8336 (tpp) cc_final: 0.8038 (tpp)
REVERT: A  256 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8239 (tm-30)
REVERT: A  523 ASP cc_start: 0.8066 (t70) cc_final: 0.7727 (t70)
REVERT: B  165 MET cc_start: 0.8460 (tpp) cc_final: 0.8172 (tpp)
REVERT: B  256 GLN cc_start: 0.8350 (tm-30) cc_final: 0.7988 (tm-30)
REVERT: B  389 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.6592 (t80)
REVERT: B  531 GLU cc_start: 0.7813 (tp30) cc_final: 0.7585 (tp30)
REVERT: B  559 MET cc_start: 0.8017 (tpp) cc_final: 0.7744 (tpp)
  outliers start: 17
  outliers final: 12
  residues processed: 195
  average time/residue: 0.1859
  time to fit residues: 55.2493
Evaluate side-chains
  183 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 170
  time to evaluate  : 1.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  646 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 111 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 639 GLN
B 639 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.137346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.103485 restraints weight = 17321.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.106460 restraints weight = 9804.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.108308 restraints weight = 6982.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10440  Z= 0.217
  Angle     :  0.628  13.376  14200  Z= 0.308
  Chirality :  0.042   0.150   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  4.048  19.492   1360
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.41 %
    Favored  : 82.61 %
  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:  1.15 (0.25), residues: 1248
  helix:  1.97 (0.17), residues: 872
  sheet: -2.48 (0.80), residues: 36
  loop : -2.20 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 624 
 HIS   0.003   0.001   HIS B 628 
 PHE   0.029   0.001   PHE B 428 
 TYR   0.012   0.001   TYR A 468 
 ARG   0.002   0.000   ARG A 309 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 181
  time to evaluate  : 1.304 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.8462 (p0) cc_final: 0.7983 (p0)
REVERT: A  165 MET cc_start: 0.8498 (tpp) cc_final: 0.8242 (tpp)
REVERT: A  256 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8216 (tm-30)
REVERT: B  165 MET cc_start: 0.8453 (tpp) cc_final: 0.8125 (tpp)
REVERT: B  256 GLN cc_start: 0.8348 (tm-30) cc_final: 0.7950 (tm-30)
REVERT: B  389 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.6631 (t80)
REVERT: B  531 GLU cc_start: 0.7850 (tp30) cc_final: 0.7562 (tp30)
  outliers start: 21
  outliers final: 16
  residues processed: 190
  average time/residue: 0.1795
  time to fit residues: 52.1753
Evaluate side-chains
  186 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 169
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  646 LEU
Chi-restraints excluded: chain B residue  672 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 123 optimal weight:    1.9990
   chunk 120 optimal weight:    0.0060
   chunk 83 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 3 optimal weight:    6.9990
   chunk 114 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0070
   overall best weight:    0.5414

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

Flipped N/Q/H residues before XYZ refinement:
A 344 ASN
A 639 GLN
B 639 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.139828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.106164 restraints weight = 17300.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.109163 restraints weight = 9785.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.110796 restraints weight = 6952.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10440  Z= 0.171
  Angle     :  0.626  15.684  14200  Z= 0.300
  Chirality :  0.041   0.151   1604
  Planarity :  0.005   0.052   1762
  Dihedral  :  3.996  19.900   1360
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 16.54 %
    Favored  : 81.85 %
  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:  1.20 (0.24), residues: 1248
  helix:  1.98 (0.17), residues: 872
  sheet: -2.45 (0.80), residues: 36
  loop : -2.11 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 624 
 HIS   0.002   0.000   HIS A 379 
 PHE   0.025   0.001   PHE B 159 
 TYR   0.010   0.001   TYR A 468 
 ARG   0.005   0.000   ARG A  36 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 190
  time to evaluate  : 1.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.8460 (p0) cc_final: 0.7980 (p0)
REVERT: A  165 MET cc_start: 0.8573 (tpp) cc_final: 0.8291 (tpp)
REVERT: A  256 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8217 (tm-30)
REVERT: A  523 ASP cc_start: 0.8127 (t70) cc_final: 0.7770 (t70)
REVERT: B  165 MET cc_start: 0.8518 (tpp) cc_final: 0.8183 (tpp)
REVERT: B  256 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7917 (tm-30)
REVERT: B  389 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.6533 (t80)
  outliers start: 17
  outliers final: 11
  residues processed: 196
  average time/residue: 0.1836
  time to fit residues: 54.6029
Evaluate side-chains
  185 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 173
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  178 MET
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  586 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 85 optimal weight:   30.0000
   chunk 62 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 82 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   chunk 68 optimal weight:    0.8980
   chunk 115 optimal weight:    1.9990
   chunk 120 optimal weight:    0.3980
   chunk 3 optimal weight:    7.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
A 639 GLN
B 615 GLN
B 639 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.134544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.100080 restraints weight = 17610.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.103082 restraints weight = 9840.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.104947 restraints weight = 6940.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  10440  Z= 0.322
  Angle     :  0.696  14.310  14200  Z= 0.342
  Chirality :  0.045   0.165   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  4.103  19.153   1360
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.26 %
    Favored  : 81.47 %
  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:  1.15 (0.25), residues: 1248
  helix:  1.96 (0.18), residues: 874
  sheet: -2.51 (0.81), residues: 36
  loop : -2.18 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 525 
 HIS   0.005   0.001   HIS A 379 
 PHE   0.039   0.002   PHE B 451 
 TYR   0.015   0.001   TYR A 468 
 ARG   0.003   0.000   ARG A 374 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 172
  time to evaluate  : 1.143 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.8457 (p0) cc_final: 0.7982 (p0)
REVERT: A  165 MET cc_start: 0.8591 (tpp) cc_final: 0.8266 (tpp)
REVERT: A  256 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8154 (tm-30)
REVERT: A  559 MET cc_start: 0.7984 (tpp) cc_final: 0.7659 (tpp)
REVERT: B  165 MET cc_start: 0.8522 (tpp) cc_final: 0.8162 (tpp)
REVERT: B  256 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7871 (tm-30)
REVERT: B  297 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8013 (pm20)
REVERT: B  389 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7479 (t80)
  outliers start: 24
  outliers final: 16
  residues processed: 186
  average time/residue: 0.1734
  time to fit residues: 50.4488
Evaluate side-chains
  186 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 168
  time to evaluate  : 1.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  293 HIS
Chi-restraints excluded: chain A residue  344 ASN
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  472 ASN
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  665 THR
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  344 ASN
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  478 LEU
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  672 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 116 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 42 optimal weight:    0.0030
   chunk 77 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 86 optimal weight:    9.9990
   chunk 46 optimal weight:    8.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
A 639 GLN
B 344 ASN
B 639 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.138400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.104719 restraints weight = 17291.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.107619 restraints weight = 9767.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.109489 restraints weight = 6953.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
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   0.032  10440  Z= 0.190
  Angle     :  0.662  14.478  14200  Z= 0.317
  Chirality :  0.042   0.190   1604
  Planarity :  0.005   0.052   1762
  Dihedral  :  4.073  21.974   1360
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 17.39 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.19 (0.25), residues: 1248
  helix:  1.94 (0.17), residues: 872
  sheet: -2.48 (0.80), residues: 36
  loop : -2.00 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 525 
 HIS   0.002   0.000   HIS A 379 
 PHE   0.031   0.001   PHE B 451 
 TYR   0.009   0.001   TYR A 468 
 ARG   0.005   0.000   ARG A 374 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 183
  time to evaluate  : 1.239 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.8425 (p0) cc_final: 0.7937 (p0)
REVERT: A  165 MET cc_start: 0.8587 (tpp) cc_final: 0.8307 (tpp)
REVERT: A  256 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8127 (tm-30)
REVERT: A  375 ARG cc_start: 0.8804 (tpp80) cc_final: 0.8597 (mmt-90)
REVERT: B  169 PHE cc_start: 0.7467 (m-80) cc_final: 0.7257 (m-80)
REVERT: B  256 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7885 (tm-30)
REVERT: B  297 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8049 (pm20)
REVERT: B  389 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7297 (t80)
  outliers start: 16
  outliers final: 8
  residues processed: 193
  average time/residue: 0.1689
  time to fit residues: 50.1851
Evaluate side-chains
  176 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 166
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  586 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 108 optimal weight:    5.9990
   chunk 110 optimal weight:    7.9990
   chunk 27 optimal weight:    0.0970
   chunk 79 optimal weight:    0.0980
   chunk 44 optimal weight:    5.9990
   chunk 111 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 639 GLN
** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 639 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.139412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.105584 restraints weight = 17356.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.108497 restraints weight = 9827.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.110401 restraints weight = 7004.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10440  Z= 0.186
  Angle     :  0.669  14.465  14200  Z= 0.318
  Chirality :  0.043   0.226   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  4.007  19.315   1360
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 17.77 %
    Favored  : 80.72 %
  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:  1.18 (0.25), residues: 1248
  helix:  1.91 (0.17), residues: 872
  sheet: -2.44 (0.80), residues: 36
  loop : -1.94 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 525 
 HIS   0.002   0.000   HIS A 379 
 PHE   0.032   0.001   PHE B 428 
 TYR   0.011   0.001   TYR B 167 
 ARG   0.006   0.000   ARG A 374 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 176
  time to evaluate  : 1.418 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.8412 (p0) cc_final: 0.7914 (p0)
REVERT: A  165 MET cc_start: 0.8587 (tpp) cc_final: 0.8260 (tpp)
REVERT: A  256 GLN cc_start: 0.8394 (tm-30) cc_final: 0.8101 (tm-30)
REVERT: B  256 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7901 (tm-30)
REVERT: B  297 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7991 (pm20)
REVERT: B  389 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7108 (t80)
REVERT: B  533 LEU cc_start: 0.9335 (mt) cc_final: 0.9099 (mt)
  outliers start: 16
  outliers final: 8
  residues processed: 185
  average time/residue: 0.1718
  time to fit residues: 50.2626
Evaluate side-chains
  180 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 170
  time to evaluate  : 1.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  672 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 109 optimal weight:    7.9990
   chunk 70 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   chunk 42 optimal weight:    0.3980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 639 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.139730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.105669 restraints weight = 17183.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.108607 restraints weight = 9778.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.110460 restraints weight = 6912.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10440  Z= 0.189
  Angle     :  0.662  14.173  14200  Z= 0.314
  Chirality :  0.043   0.201   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  3.969  19.218   1360
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 18.24 %
    Favored  : 80.34 %
  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:  1.17 (0.25), residues: 1248
  helix:  1.99 (0.18), residues: 860
  sheet: -2.41 (0.81), residues: 36
  loop : -2.07 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 525 
 HIS   0.003   0.001   HIS A 232 
 PHE   0.033   0.001   PHE B 169 
 TYR   0.011   0.001   TYR A 468 
 ARG   0.003   0.000   ARG B 682 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2915.85 seconds
wall clock time: 53 minutes 20.41 seconds (3200.41 seconds total)