Starting phenix.real_space_refine
on Thu May  1 01:26:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xw2_38728/05_2025/8xw2_38728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xw2_38728/05_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_38728/05_2025/8xw2_38728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xw2_38728/05_2025/8xw2_38728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xw2_38728/05_2025/8xw2_38728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xw2_38728/05_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-5669/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: 9.40, per 1000 atoms: 0.93
  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: 2.60
  Conformation dependent library (CDL) restraints added in 1.1 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: 1.12
  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: 3.01

  Time building geometry restraints manager: 3.05 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:             0.830
  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:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     28.810
  Find NCS groups from input model:        0.180
  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:             0.010
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.330
-------------------------------------------------------------------------------
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= 0.207
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08065 (  691)
  hydrogen bonds       : angle       4.88464 ( 2049)
  covalent geometry    : bond        0.00459 (10440)
  covalent geometry    : angle       0.75562 (14200)

*********************** 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  : 1.085 
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: 0.1753
  time to fit residues: 59.6467
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  : 1.187 
-------------------------------------------------------------------------------
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 = 0.3255 r_free = 0.3255 target = 0.103403 restraints weight = 17271.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.106367 restraints weight = 9788.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.107964 restraints weight = 6982.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
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= 0.142
  Angle     :  0.655  12.985  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04058 (  691)
  hydrogen bonds       : angle       4.46176 ( 2049)
  covalent geometry    : bond        0.00313 (10440)
  covalent geometry    : angle       0.65491 (14200)

*********************** 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  : 1.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 SER cc_start: 0.8138 (p) cc_final: 0.7706 (m)
REVERT: A   74 ASN cc_start: 0.8466 (p0) cc_final: 0.7854 (p0)
REVERT: A  102 TYR cc_start: 0.8671 (m-10) cc_final: 0.8436 (m-80)
REVERT: A  165 MET cc_start: 0.8071 (tpt) cc_final: 0.7667 (ttt)
REVERT: A  256 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8188 (tm-30)
REVERT: A  559 MET cc_start: 0.8304 (tpt) cc_final: 0.7649 (tpt)
REVERT: A  643 MET cc_start: 0.7879 (tmm) cc_final: 0.7505 (tmm)
REVERT: B   40 SER cc_start: 0.8184 (p) cc_final: 0.7934 (m)
REVERT: B  256 GLN cc_start: 0.8347 (tm-30) cc_final: 0.8001 (tm-30)
REVERT: B  643 MET cc_start: 0.8075 (tmm) cc_final: 0.7873 (tmm)
  outliers start: 12
  outliers final: 7
  residues processed: 201
  average time/residue: 0.1706
  time to fit residues: 52.2894
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  : 1.121 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 85 optimal weight:   40.0000
   chunk 22 optimal weight:   30.0000
   chunk 65 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   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 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 = 0.3707 r_free = 0.3707 target = 0.136276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.102653 restraints weight = 17468.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.105538 restraints weight = 9966.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.107373 restraints weight = 7097.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.1595

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= 0.146
  Angle     :  0.629  13.332  14200  Z= 0.312
  Chirality :  0.043   0.154   1604
  Planarity :  0.005   0.056   1762
  Dihedral  :  4.242  18.774   1360
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.19 %
    Favored  : 86.11 %
  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:  0.90 (0.24), residues: 1248
  helix:  1.94 (0.18), residues: 846
  sheet: -2.47 (0.73), residues: 36
  loop : -2.45 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 624 
 HIS   0.003   0.001   HIS B 628 
 PHE   0.026   0.001   PHE A 159 
 TYR   0.014   0.001   TYR A 468 
 ARG   0.002   0.000   ARG B 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03891 (  691)
  hydrogen bonds       : angle       4.40384 ( 2049)
  covalent geometry    : bond        0.00344 (10440)
  covalent geometry    : angle       0.62853 (14200)

*********************** 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
  204 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 186
  time to evaluate  : 1.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 SER cc_start: 0.8164 (p) cc_final: 0.7791 (m)
REVERT: A   74 ASN cc_start: 0.8454 (p0) cc_final: 0.7865 (p0)
REVERT: A  256 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8229 (tm-30)
REVERT: A  559 MET cc_start: 0.8273 (tpt) cc_final: 0.7902 (tpt)
REVERT: B  165 MET cc_start: 0.7964 (tpp) cc_final: 0.7541 (ttp)
REVERT: B  256 GLN cc_start: 0.8387 (tm-30) cc_final: 0.8014 (tm-30)
REVERT: B  559 MET cc_start: 0.8264 (tpp) cc_final: 0.6937 (ppp)
  outliers start: 18
  outliers final: 12
  residues processed: 198
  average time/residue: 0.1696
  time to fit residues: 51.5952
Evaluate side-chains
  188 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 176
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
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  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  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:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 92 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 47 optimal weight:    7.9990
   chunk 15 optimal weight:    0.0770
   chunk 28 optimal weight:    3.9990
   chunk 101 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    1.1542

-------------------------------------------------------------------------------
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 = 0.3707 r_free = 0.3707 target = 0.136192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.102323 restraints weight = 17329.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.105207 restraints weight = 9817.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.107079 restraints weight = 7029.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10440  Z= 0.147
  Angle     :  0.630  13.153  14200  Z= 0.313
  Chirality :  0.043   0.151   1604
  Planarity :  0.005   0.055   1762
  Dihedral  :  4.176  19.208   1360
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 13.52 %
    Favored  : 84.22 %
  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:  0.97 (0.24), residues: 1248
  helix:  1.93 (0.18), residues: 860
  sheet: -2.60 (0.74), residues: 36
  loop : -2.39 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 624 
 HIS   0.003   0.001   HIS A 293 
 PHE   0.026   0.001   PHE B 159 
 TYR   0.012   0.001   TYR A 468 
 ARG   0.001   0.000   ARG A  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03768 (  691)
  hydrogen bonds       : angle       4.40267 ( 2049)
  covalent geometry    : bond        0.00346 (10440)
  covalent geometry    : angle       0.63020 (14200)

*********************** 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
  205 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 181
  time to evaluate  : 1.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 SER cc_start: 0.8161 (p) cc_final: 0.7802 (m)
REVERT: A   74 ASN cc_start: 0.8445 (p0) cc_final: 0.7877 (p0)
REVERT: A  165 MET cc_start: 0.8297 (tpp) cc_final: 0.8030 (tpp)
REVERT: A  256 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8201 (tm-30)
REVERT: A  559 MET cc_start: 0.8250 (tpt) cc_final: 0.7933 (tpt)
REVERT: B  165 MET cc_start: 0.8381 (tpp) cc_final: 0.8053 (tpp)
REVERT: B  256 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7962 (tm-30)
REVERT: B  389 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7258 (t80)
  outliers start: 24
  outliers final: 17
  residues processed: 194
  average time/residue: 0.1682
  time to fit residues: 50.2836
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  : 1.115 
-------------------------------------------------------------------------------
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  396 VAL
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  665 THR
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  472 ASN
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 111 optimal weight:    0.0770
   chunk 32 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 81 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0570
   chunk 20 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   overall best weight:    0.4856

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.139114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.105383 restraints weight = 17069.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.108289 restraints weight = 9715.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.110141 restraints weight = 6957.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10440  Z= 0.115
  Angle     :  0.611  15.089  14200  Z= 0.296
  Chirality :  0.041   0.151   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  4.060  19.722   1360
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.74 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.24), residues: 1248
  helix:  1.94 (0.17), residues: 872
  sheet: -2.50 (0.76), residues: 36
  loop : -2.24 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 624 
 HIS   0.001   0.000   HIS B 714 
 PHE   0.028   0.001   PHE B 159 
 TYR   0.010   0.001   TYR A 468 
 ARG   0.002   0.000   ARG B 309 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03453 (  691)
  hydrogen bonds       : angle       4.33015 ( 2049)
  covalent geometry    : bond        0.00253 (10440)
  covalent geometry    : angle       0.61067 (14200)

*********************** 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
  217 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 198
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.8428 (p0) cc_final: 0.7915 (p0)
REVERT: A  102 TYR cc_start: 0.8596 (m-10) cc_final: 0.8393 (m-80)
REVERT: A  165 MET cc_start: 0.8420 (tpp) cc_final: 0.8148 (tpp)
REVERT: A  256 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8232 (tm-30)
REVERT: A  523 ASP cc_start: 0.8057 (t70) cc_final: 0.7720 (t70)
REVERT: A  643 MET cc_start: 0.7993 (tmm) cc_final: 0.7748 (tmm)
REVERT: B  165 MET cc_start: 0.8480 (tpp) cc_final: 0.8189 (tpp)
REVERT: B  256 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8028 (tm-30)
REVERT: B  389 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.6612 (t80)
REVERT: B  559 MET cc_start: 0.8031 (tpp) cc_final: 0.7824 (tpp)
  outliers start: 19
  outliers final: 12
  residues processed: 205
  average time/residue: 0.1855
  time to fit residues: 58.4783
Evaluate side-chains
  184 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 171
  time to evaluate  : 1.208 
-------------------------------------------------------------------------------
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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 111 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    1.3786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.136479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.102577 restraints weight = 17225.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.105421 restraints weight = 9861.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.107257 restraints weight = 7094.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10440  Z= 0.158
  Angle     :  0.641  13.213  14200  Z= 0.316
  Chirality :  0.043   0.163   1604
  Planarity :  0.005   0.054   1762
  Dihedral  :  4.051  19.212   1360
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 16.16 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.25), residues: 1248
  helix:  1.95 (0.17), residues: 872
  sheet: -2.50 (0.80), residues: 36
  loop : -2.25 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 624 
 HIS   0.003   0.001   HIS B 628 
 PHE   0.025   0.001   PHE B 159 
 TYR   0.018   0.001   TYR B 181 
 ARG   0.002   0.000   ARG A 309 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03633 (  691)
  hydrogen bonds       : angle       4.36284 ( 2049)
  covalent geometry    : bond        0.00373 (10440)
  covalent geometry    : angle       0.64059 (14200)

*********************** 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
  196 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 177
  time to evaluate  : 1.126 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.8459 (p0) cc_final: 0.7975 (p0)
REVERT: A  165 MET cc_start: 0.8447 (tpp) cc_final: 0.8182 (tpp)
REVERT: A  256 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8208 (tm-30)
REVERT: B  165 MET cc_start: 0.8454 (tpp) cc_final: 0.8095 (tpp)
REVERT: B  256 GLN cc_start: 0.8341 (tm-30) cc_final: 0.7929 (tm-30)
REVERT: B  389 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7209 (t80)
REVERT: B  559 MET cc_start: 0.8095 (tpp) cc_final: 0.7868 (tpp)
  outliers start: 19
  outliers final: 12
  residues processed: 184
  average time/residue: 0.1617
  time to fit residues: 46.2429
Evaluate side-chains
  182 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 169
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  472 ASN
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 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 123 optimal weight:    0.8980
   chunk 120 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 3 optimal weight:    6.9990
   chunk 114 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9980
   chunk 94 optimal weight:    0.8980
   overall best weight:    0.8380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.138229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.104427 restraints weight = 17290.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.107333 restraints weight = 9789.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.109198 restraints weight = 6975.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.2296

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= 0.129
  Angle     :  0.637  15.390  14200  Z= 0.307
  Chirality :  0.042   0.152   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  4.029  19.584   1360
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 16.64 %
    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 (0.24), residues: 1248
  helix:  1.97 (0.17), residues: 872
  sheet: -2.54 (0.78), residues: 36
  loop : -2.16 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 624 
 HIS   0.002   0.001   HIS B 628 
 PHE   0.030   0.001   PHE B 428 
 TYR   0.014   0.001   TYR B 181 
 ARG   0.002   0.000   ARG A  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03501 (  691)
  hydrogen bonds       : angle       4.32971 ( 2049)
  covalent geometry    : bond        0.00296 (10440)
  covalent geometry    : angle       0.63710 (14200)

*********************** 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
  204 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 184
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.8436 (p0) cc_final: 0.7949 (p0)
REVERT: A  165 MET cc_start: 0.8504 (tpp) cc_final: 0.8247 (tpp)
REVERT: A  256 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8172 (tm-30)
REVERT: A  643 MET cc_start: 0.7994 (tmm) cc_final: 0.7776 (tmm)
REVERT: B  165 MET cc_start: 0.8463 (tpp) cc_final: 0.8144 (tpp)
REVERT: B  256 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7869 (tm-30)
REVERT: B  389 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7065 (t80)
  outliers start: 20
  outliers final: 13
  residues processed: 192
  average time/residue: 0.1585
  time to fit residues: 47.8591
Evaluate side-chains
  187 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 173
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
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  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 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  681 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 86 optimal weight:    6.9990
   chunk 85 optimal weight:   30.0000
   chunk 62 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 92 optimal weight:    0.0570
   chunk 68 optimal weight:    0.0270
   chunk 115 optimal weight:    0.6980
   chunk 120 optimal weight:    0.9990
   chunk 3 optimal weight:    7.9990
   overall best weight:    0.5358

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.139353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.105496 restraints weight = 17404.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.108456 restraints weight = 9785.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.110254 restraints weight = 6953.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10440  Z= 0.120
  Angle     :  0.640  14.814  14200  Z= 0.309
  Chirality :  0.042   0.168   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  3.998  20.115   1360
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.20 %
    Favored  : 80.91 %
  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: -2.52 (0.78), residues: 36
  loop : -2.10 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 624 
 HIS   0.003   0.001   HIS A 379 
 PHE   0.031   0.001   PHE B 428 
 TYR   0.011   0.001   TYR B 181 
 ARG   0.005   0.000   ARG A 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03396 (  691)
  hydrogen bonds       : angle       4.33173 ( 2049)
  covalent geometry    : bond        0.00266 (10440)
  covalent geometry    : angle       0.64001 (14200)

*********************** 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
  210 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 190
  time to evaluate  : 1.171 
Fit side-chains
REVERT: A   74 ASN cc_start: 0.8450 (p0) cc_final: 0.7973 (p0)
REVERT: A  165 MET cc_start: 0.8565 (tpp) cc_final: 0.8295 (tpp)
REVERT: A  256 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8158 (tm-30)
REVERT: A  559 MET cc_start: 0.8015 (tpp) cc_final: 0.7718 (tpp)
REVERT: A  643 MET cc_start: 0.7975 (tmm) cc_final: 0.7757 (tmm)
REVERT: B  165 MET cc_start: 0.8498 (tpp) cc_final: 0.8235 (tpp)
REVERT: B  256 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7879 (tm-30)
REVERT: B  389 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7019 (t80)
  outliers start: 20
  outliers final: 11
  residues processed: 197
  average time/residue: 0.1654
  time to fit residues: 50.3643
Evaluate side-chains
  190 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 178
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
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  434 LEU
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  578 LEU
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  478 LEU
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  681 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 113 optimal weight:    0.6980
   chunk 2 optimal weight:    8.9990
   chunk 42 optimal weight:    0.0270
   chunk 77 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 86 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   chunk 21 optimal weight:   30.0000
   overall best weight:    0.9042

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.138263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.103984 restraints weight = 17440.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.106954 restraints weight = 9813.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.108839 restraints weight = 6977.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2526

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= 0.135
  Angle     :  0.656  14.265  14200  Z= 0.317
  Chirality :  0.042   0.161   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  3.995  19.956   1360
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 17.49 %
    Favored  : 80.81 %
  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 (0.24), residues: 1248
  helix:  1.96 (0.17), residues: 872
  sheet: -2.48 (0.80), residues: 36
  loop : -2.10 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 525 
 HIS   0.002   0.001   HIS B 628 
 PHE   0.032   0.001   PHE B 428 
 TYR   0.015   0.001   TYR B 181 
 ARG   0.004   0.000   ARG B 682 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03524 (  691)
  hydrogen bonds       : angle       4.33142 ( 2049)
  covalent geometry    : bond        0.00310 (10440)
  covalent geometry    : angle       0.65615 (14200)

*********************** 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
  197 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 179
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.8424 (p0) cc_final: 0.7946 (p0)
REVERT: A  165 MET cc_start: 0.8561 (tpp) cc_final: 0.8259 (tpp)
REVERT: A  256 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8127 (tm-30)
REVERT: A  559 MET cc_start: 0.7820 (tpp) cc_final: 0.7576 (tpp)
REVERT: A  643 MET cc_start: 0.8010 (tmm) cc_final: 0.7780 (tmm)
REVERT: B  165 MET cc_start: 0.8494 (tpp) cc_final: 0.8278 (tpp)
REVERT: B  256 GLN cc_start: 0.8287 (tm-30) cc_final: 0.7871 (tm-30)
REVERT: B  389 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7077 (t80)
  outliers start: 18
  outliers final: 13
  residues processed: 189
  average time/residue: 0.1609
  time to fit residues: 48.4384
Evaluate side-chains
  188 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 174
  time to evaluate  : 1.271 
-------------------------------------------------------------------------------
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  311 GLU
Chi-restraints excluded: chain A residue  432 ILE
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 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  478 LEU
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:    0.7980
   chunk 4 optimal weight:    0.2980
   chunk 108 optimal weight:    0.0000
   chunk 110 optimal weight:    8.9990
   chunk 27 optimal weight:    0.0040
   chunk 79 optimal weight:    0.5980
   chunk 44 optimal weight:    4.9990
   chunk 111 optimal weight:    0.7980
   chunk 88 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.3396

-------------------------------------------------------------------------------
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 = 0.3763 r_free = 0.3763 target = 0.140732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.106825 restraints weight = 17351.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.109858 restraints weight = 9779.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.111736 restraints weight = 6945.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10440  Z= 0.117
  Angle     :  0.647  14.197  14200  Z= 0.308
  Chirality :  0.042   0.200   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  3.945  20.847   1360
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 17.96 %
    Favored  : 80.43 %
  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 (0.24), residues: 1248
  helix:  2.02 (0.17), residues: 862
  sheet: -2.43 (0.79), residues: 36
  loop : -2.15 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 525 
 HIS   0.002   0.000   HIS B 232 
 PHE   0.032   0.001   PHE B 428 
 TYR   0.010   0.001   TYR A 468 
 ARG   0.005   0.000   ARG A 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03341 (  691)
  hydrogen bonds       : angle       4.27967 ( 2049)
  covalent geometry    : bond        0.00248 (10440)
  covalent geometry    : angle       0.64702 (14200)

********************** 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
  209 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 192
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.8416 (p0) cc_final: 0.7934 (p0)
REVERT: A  165 MET cc_start: 0.8548 (tpp) cc_final: 0.8226 (tpp)
REVERT: A  256 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8141 (tm-30)
REVERT: A  376 LEU cc_start: 0.8718 (mm) cc_final: 0.8476 (mm)
REVERT: A  523 ASP cc_start: 0.8162 (t70) cc_final: 0.7811 (t70)
REVERT: A  643 MET cc_start: 0.7971 (tmm) cc_final: 0.7737 (tmm)
REVERT: B  256 GLN cc_start: 0.8305 (tm-30) cc_final: 0.7882 (tm-30)
REVERT: B  389 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.6669 (t80)
  outliers start: 17
  outliers final: 10
  residues processed: 199
  average time/residue: 0.1781
  time to fit residues: 56.6204
Evaluate side-chains
  190 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 179
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  293 HIS
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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 80 optimal weight:    0.2980
   chunk 34 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 109 optimal weight:    4.9990
   chunk 70 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 42 optimal weight:    0.4980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.140150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.105988 restraints weight = 17277.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.109033 restraints weight = 9711.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.110910 restraints weight = 6888.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10440  Z= 0.123
  Angle     :  0.658  13.817  14200  Z= 0.313
  Chirality :  0.043   0.226   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  3.931  20.451   1360
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 18.62 %
    Favored  : 79.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.00 (0.17), residues: 862
  sheet: -2.42 (0.79), residues: 36
  loop : -2.11 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP B 525 
 HIS   0.003   0.000   HIS A 232 
 PHE   0.032   0.001   PHE B 428 
 TYR   0.012   0.001   TYR B 181 
 ARG   0.004   0.000   ARG B 682 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03405 (  691)
  hydrogen bonds       : angle       4.28337 ( 2049)
  covalent geometry    : bond        0.00277 (10440)
  covalent geometry    : angle       0.65771 (14200)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3255.35 seconds
wall clock time: 58 minutes 6.86 seconds (3486.86 seconds total)