Starting phenix.real_space_refine
on Fri Aug 22 18:55:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b0p_15791/08_2025/8b0p_15791.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b0p_15791/08_2025/8b0p_15791.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b0p_15791/08_2025/8b0p_15791.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b0p_15791/08_2025/8b0p_15791.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b0p_15791/08_2025/8b0p_15791.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b0p_15791/08_2025/8b0p_15791.cif"
  }
  resolution = 2.86
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.001 sd=   0.045
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3779 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    2652      2.51       5
     N     655      2.21       5
     O     695      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4016
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3911
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 505, 3911
          Classifications: {'peptide': 505}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 36, 'TRANS': 468}
          Unresolved non-hydrogen bonds: 62
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 53
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 1, 'PHE:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 39
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 43
          Classifications: {'peptide': 5}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 4}
    Chain: "B"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 62
          Unusual residues: {'IG7': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'IG7:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 1.04, per 1000 atoms: 0.26
  Number of scatterers: 4016
  At special positions: 0
  Unit cell: (57.82, 83.426, 85.904, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      14     16.00
     O     695      8.00
     N     655      7.00
     C    2652      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.35
  Conformation dependent library (CDL) restraints added in 101.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  SER B   2 "
        pdb=" CB  LYS B   3 "
  Number of C-beta restraints generated:  936

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 4 sheets defined
      55.3% alpha, 13.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 24
      removed outlier: 3.737A  pdb=" N   LEU A  18 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LEU A  19 " --> pdb=" O   LEU A  15 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLY A  24 " --> pdb=" O   PHE A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 28
      removed outlier: 3.544A  pdb=" N   PHE A  28 " --> pdb=" O   THR A  25 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 25 through 28'
    Processing helix  chain 'A' and resid 33 through 48
      removed outlier: 3.998A  pdb=" N   ALA A  37 " --> pdb=" O   VAL A  33 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ILE A  38 " --> pdb=" O   TRP A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 69
    Processing helix  chain 'A' and resid 74 through 82
      removed outlier: 3.904A  pdb=" N   SER A  78 " --> pdb=" O   TRP A  74 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   PHE A  82 " --> pdb=" O   SER A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 116
      removed outlier: 4.179A  pdb=" N   TYR A 104 " --> pdb=" O   TYR A 100 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   THR A 105 " --> pdb=" O   LEU A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 126
    Processing helix  chain 'A' and resid 126 through 140
      removed outlier: 3.795A  pdb=" N   ALA A 130 " --> pdb=" O   ILE A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 145
    Processing helix  chain 'A' and resid 150 through 156
    Processing helix  chain 'A' and resid 160 through 162
      No H-bonds generated for 'chain 'A' and resid 160 through 162'
    Processing helix  chain 'A' and resid 163 through 168
    Processing helix  chain 'A' and resid 168 through 190
      removed outlier: 3.572A  pdb=" N   ILE A 172 " --> pdb=" O   GLY A 168 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE A 174 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 204
      removed outlier: 4.053A  pdb=" N   LEU A 195 " --> pdb=" O   ASN A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 211
    Processing helix  chain 'A' and resid 218 through 221
    Processing helix  chain 'A' and resid 232 through 237
      removed outlier: 4.506A  pdb=" N   TRP A 237 " --> pdb=" O   GLN A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 254
      removed outlier: 4.140A  pdb=" N   ASN A 244 " --> pdb=" O   GLY A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 257
      No H-bonds generated for 'chain 'A' and resid 255 through 257'
    Processing helix  chain 'A' and resid 277 through 292
    Processing helix  chain 'A' and resid 388 through 391
    Processing helix  chain 'A' and resid 392 through 400
    Processing helix  chain 'A' and resid 420 through 437
      removed outlier: 3.661A  pdb=" N   ARG A 432 " --> pdb=" O   MET A 428 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ALA A 433 " --> pdb=" O   ALA A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 487
    Processing helix  chain 'A' and resid 488 through 507
    Processing sheet with id=AA1, first strand: chain 'A' and resid 215 through 216
    Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 273
      removed outlier: 4.020A  pdb=" N   VAL A 300 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   ASP A 272 " --> pdb=" O   VAL A 300 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   ALA A 302 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 273
      removed outlier: 4.020A  pdb=" N   VAL A 300 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   ASP A 272 " --> pdb=" O   VAL A 300 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   ALA A 302 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ILE A 263 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
      removed outlier: 8.127A  pdb=" N   GLY A 298 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU A 262 " --> pdb=" O   GLN A 223 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 375 through 376
      removed outlier: 6.543A  pdb=" N   GLU A 381 " --> pdb=" O   TYR A 406 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   LEU A 408 " --> pdb=" O   GLU A 381 " (cutoff:3.500A)
      removed outlier: 5.831A  pdb=" N   THR A 383 " --> pdb=" O   LEU A 408 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   ILE A 410 " --> pdb=" O   THR A 383 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   ALA A 385 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
      removed outlier: 7.741A  pdb=" N   SER A 443 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   THR A 409 " --> pdb=" O   SER A 443 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   VAL A 451 " --> pdb=" O   GLN A 459 " (cutoff:3.500A)

    206 hydrogen bonds defined for protein.
    558 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: 0.64

  Time building geometry restraints manager: 0.44 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 649
        1.32 -     1.45: 1103
        1.45 -     1.57: 2348
        1.57 -     1.69: 0
        1.69 -     1.81: 26
  Bond restraints: 4126
  Sorted by residual:
  bond pdb=" C45 IG7 B   1 "
       pdb=" C46 IG7 B   1 "
    ideal  model  delta    sigma   weight residual
    1.538  1.497  0.041 2.00e-02 2.50e+03 4.30e+00
  bond pdb=" C03 IG7 B   1 "
       pdb=" C04 IG7 B   1 "
    ideal  model  delta    sigma   weight residual
    1.535  1.494  0.041 2.00e-02 2.50e+03 4.11e+00
  bond pdb=" C42 IG7 B   1 "
       pdb=" O43 IG7 B   1 "
    ideal  model  delta    sigma   weight residual
    1.428  1.458 -0.030 2.00e-02 2.50e+03 2.29e+00
  bond pdb=" C14 IG7 B   1 "
       pdb=" C15 IG7 B   1 "
    ideal  model  delta    sigma   weight residual
    1.534  1.506  0.028 2.00e-02 2.50e+03 1.90e+00
  bond pdb=" C22 IG7 B   1 "
       pdb=" C23 IG7 B   1 "
    ideal  model  delta    sigma   weight residual
    1.520  1.494  0.026 2.00e-02 2.50e+03 1.63e+00
  ... (remaining 4121 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 5504
        1.50 -     3.01: 83
        3.01 -     4.51: 27
        4.51 -     6.02: 7
        6.02 -     7.52: 2
  Bond angle restraints: 5623
  Sorted by residual:
  angle pdb=" O   LYS B   6 "
        pdb=" C   LYS B   6 "
        pdb=" OXT LYS B   6 "
      ideal   model   delta    sigma   weight residual
     118.00  125.52   -7.52 3.00e+00 1.11e-01 6.28e+00
  angle pdb=" N   ILE A 390 "
        pdb=" CA  ILE A 390 "
        pdb=" C   ILE A 390 "
      ideal   model   delta    sigma   weight residual
     113.07  109.73    3.34 1.36e+00 5.41e-01 6.02e+00
  angle pdb=" N   LYS B   6 "
        pdb=" CA  LYS B   6 "
        pdb=" CB  LYS B   6 "
      ideal   model   delta    sigma   weight residual
     110.50  114.14   -3.64 1.70e+00 3.46e-01 4.58e+00
  angle pdb=" C42 IG7 B   1 "
        pdb=" C41 IG7 B   1 "
        pdb=" S40 IG7 B   1 "
      ideal   model   delta    sigma   weight residual
     118.03  112.48    5.55 3.00e+00 1.11e-01 3.42e+00
  angle pdb=" N   LYS B   4 "
        pdb=" CA  LYS B   4 "
        pdb=" CB  LYS B   4 "
      ideal   model   delta    sigma   weight residual
     110.49  113.59   -3.10 1.69e+00 3.50e-01 3.37e+00
  ... (remaining 5618 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.83: 2412
       35.83 -    71.66: 22
       71.66 -   107.49: 6
      107.49 -   143.32: 0
      143.32 -   179.15: 1
  Dihedral angle restraints: 2441
    sinusoidal: 980
      harmonic: 1461
  Sorted by residual:
  dihedral pdb=" C04 IG7 B   1 "
           pdb=" C02 IG7 B   1 "
           pdb=" C03 IG7 B   1 "
           pdb=" O18 IG7 B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
      56.62 -122.53  179.15     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" CA  PHE A  28 "
           pdb=" C   PHE A  28 "
           pdb=" N   SER A  29 "
           pdb=" CA  SER A  29 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.31  -19.69     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" C23 IG7 B   1 "
           pdb=" C21 IG7 B   1 "
           pdb=" C22 IG7 B   1 "
           pdb=" O36 IG7 B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
      31.18  -68.78   99.96     1      3.00e+01 1.11e-03 1.25e+01
  ... (remaining 2438 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.003: 632
       1.003 -    2.006: 0
       2.006 -    3.009: 0
       3.009 -    4.012: 0
       4.012 -    5.015: 3
  Chirality restraints: 635
  Sorted by residual:
  chirality pdb=" CA  SER B   2 "
            pdb=" N   SER B   2 "
            pdb=" C   SER B   2 "
            pdb=" CB  SER B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.50    5.01 2.00e-01 2.50e+01 6.29e+02
  chirality pdb=" CA  LYS B   3 "
            pdb=" N   LYS B   3 "
            pdb=" C   LYS B   3 "
            pdb=" CB  LYS B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51   -2.31    4.82 2.00e-01 2.50e+01 5.82e+02
  chirality pdb=" C42 IG7 B   1 "
            pdb=" C19 IG7 B   1 "
            pdb=" C41 IG7 B   1 "
            pdb=" O43 IG7 B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49    2.31   -4.80 2.00e-01 2.50e+01 5.76e+02
  ... (remaining 632 not shown)

  Planarity restraints: 703
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C02 IG7 B   1 "   -0.041 2.00e-02 2.50e+03   1.14e-01 1.62e+02
        pdb=" C03 IG7 B   1 "    0.103 2.00e-02 2.50e+03
        pdb=" C38 IG7 B   1 "    0.137 2.00e-02 2.50e+03
        pdb=" N01 IG7 B   1 "   -0.183 2.00e-02 2.50e+03
        pdb=" O18 IG7 B   1 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A  87 "    0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO A  88 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A  88 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A  88 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 421 "   -0.024 5.00e-02 4.00e+02   3.57e-02 2.04e+00
        pdb=" N   PRO A 422 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A 422 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 422 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 700 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 708
        2.77 -     3.30: 3916
        3.30 -     3.83: 6836
        3.83 -     4.37: 8614
        4.37 -     4.90: 14610
  Nonbonded interactions: 34684
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 133 "
            pdb=" OG1 THR A 495 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OH  TYR A 333 "
            pdb=" OE1 GLU A 389 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   ALA A  98 "
            pdb=" OG  SER A 102 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   LEU A 143 "
            pdb=" OG1 THR A 144 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" ND2 ASN A 336 "
            pdb=" O   GLY A 368 "
     model   vdw
     2.393 3.120
  ... (remaining 34679 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     5.010
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  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:6.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   4127  Z= 0.215
  Angle     :  0.550   7.520   5623  Z= 0.267
  Chirality :  0.338   5.015    635
  Planarity :  0.006   0.114    703
  Dihedral  : 12.108 179.150   1505
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.16 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  2.68 %
    Favored  : 96.35 %
  Cbeta Deviations :  0.43 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.36), residues: 506
  helix:  0.31 (0.32), residues: 251
  sheet: -0.62 (0.65), residues: 62
  loop : -0.80 (0.44), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 193 
 TYR   0.007   0.001   TYR A 313 
 PHE   0.007   0.001   PHE A  28 
 TRP   0.008   0.001   TRP A 489 
 HIS   0.001   0.000   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 4126)
  covalent geometry    : angle       0.55042 ( 5623)
  hydrogen bonds       : bond        0.22880 (  205)
  hydrogen bonds       : angle       7.82949 (  558)
  Misc. bond           : bond        0.09332 (    1)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A   82 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.5760 (p90)
REVERT: A  170 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6921 (mp0)
REVERT: A  331 ASP cc_start: 0.7012 (m-30) cc_final: 0.6800 (m-30)
  outliers start: 4
  outliers final: 0
  residues processed: 50
  average time/residue: 0.2823
  time to fit residues: 14.9610
Evaluate side-chains
  39 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 38
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0030
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
A 223 GLN
A 307 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.129666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.116263 restraints weight = 4946.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 1.39
r_work: 0.3264 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.1281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4127  Z= 0.145
  Angle     :  0.612  10.123   5623  Z= 0.306
  Chirality :  0.067   1.268    635
  Planarity :  0.005   0.038    703
  Dihedral  : 12.961 167.447    614
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.16 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  :  5.11 %
    Favored  : 92.94 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.38), residues: 506
  helix:  0.88 (0.33), residues: 258
  sheet: -0.26 (0.64), residues: 56
  loop : -0.82 (0.47), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 193 
 TYR   0.008   0.001   TYR A 388 
 PHE   0.010   0.001   PHE A 174 
 TRP   0.009   0.001   TRP A 489 
 HIS   0.002   0.001   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4126)
  covalent geometry    : angle       0.61167 ( 5623)
  hydrogen bonds       : bond        0.04562 (  205)
  hydrogen bonds       : angle       5.41870 (  558)
  Misc. bond           : bond        0.00005 (    1)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.099 
Fit side-chains
REVERT: A   82 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.5557 (p90)
  outliers start: 8
  outliers final: 2
  residues processed: 47
  average time/residue: 0.2245
  time to fit residues: 11.2916
Evaluate side-chains
  41 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 38
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 PHE
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  297 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 35 optimal weight:    0.0570
   chunk 8 optimal weight:    0.1980
   chunk 2 optimal weight:    0.0470
   chunk 31 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 0 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.3798

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.129308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.115803 restraints weight = 4900.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 1.40
r_work: 0.3287 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4127  Z= 0.107
  Angle     :  0.547   6.282   5623  Z= 0.271
  Chirality :  0.051   0.726    635
  Planarity :  0.005   0.037    703
  Dihedral  : 11.964 134.626    614
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.57 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  :  6.08 %
    Favored  : 91.73 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.39), residues: 506
  helix:  1.11 (0.34), residues: 261
  sheet: -0.21 (0.64), residues: 56
  loop : -0.81 (0.47), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 430 
 TYR   0.006   0.001   TYR A 313 
 PHE   0.010   0.001   PHE A 174 
 TRP   0.009   0.001   TRP A 489 
 HIS   0.001   0.000   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 4126)
  covalent geometry    : angle       0.54711 ( 5623)
  hydrogen bonds       : bond        0.03573 (  205)
  hydrogen bonds       : angle       4.95795 (  558)
  Misc. bond           : bond        0.00061 (    1)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.7366 (m110) cc_final: 0.6740 (t0)
REVERT: A   82 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.5697 (p90)
REVERT: A  403 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7844 (m-30)
  outliers start: 9
  outliers final: 2
  residues processed: 47
  average time/residue: 0.2558
  time to fit residues: 12.9695
Evaluate side-chains
  41 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 37
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue   82 PHE
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  403 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 4 optimal weight:    0.2980
   chunk 26 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0970
   chunk 43 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 23 optimal weight:    7.9990
   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 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.133441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.120588 restraints weight = 4806.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 1.35
r_work: 0.3283 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4127  Z= 0.112
  Angle     :  0.539   6.066   5623  Z= 0.265
  Chirality :  0.047   0.522    635
  Planarity :  0.004   0.036    703
  Dihedral  : 11.408 114.183    614
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  :  9.25 %
    Favored  : 89.29 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.39), residues: 506
  helix:  1.20 (0.34), residues: 261
  sheet: -0.26 (0.63), residues: 56
  loop : -0.82 (0.47), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 193 
 TYR   0.007   0.001   TYR A 388 
 PHE   0.010   0.001   PHE A 174 
 TRP   0.007   0.001   TRP A 489 
 HIS   0.001   0.000   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 4126)
  covalent geometry    : angle       0.53910 ( 5623)
  hydrogen bonds       : bond        0.03324 (  205)
  hydrogen bonds       : angle       4.78557 (  558)
  Misc. bond           : bond        0.00114 (    1)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.7466 (m110) cc_final: 0.6845 (t0)
REVERT: A   82 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.5888 (p90)
  outliers start: 6
  outliers final: 1
  residues processed: 42
  average time/residue: 0.3085
  time to fit residues: 13.9136
Evaluate side-chains
  39 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 PHE
Chi-restraints excluded: chain A residue  287 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 23 optimal weight:    8.9990
   chunk 41 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 37 optimal weight:    0.4980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.132768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.119935 restraints weight = 4781.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 1.34
r_work: 0.3276 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4127  Z= 0.122
  Angle     :  0.541   6.098   5623  Z= 0.267
  Chirality :  0.046   0.421    635
  Planarity :  0.004   0.037    703
  Dihedral  : 11.182 112.736    614
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  :  9.73 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.39), residues: 506
  helix:  1.21 (0.34), residues: 262
  sheet: -0.23 (0.64), residues: 56
  loop : -0.77 (0.47), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 193 
 TYR   0.006   0.001   TYR A 104 
 PHE   0.010   0.001   PHE A 174 
 TRP   0.008   0.001   TRP A 489 
 HIS   0.001   0.000   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4126)
  covalent geometry    : angle       0.54063 ( 5623)
  hydrogen bonds       : bond        0.03357 (  205)
  hydrogen bonds       : angle       4.74117 (  558)
  Misc. bond           : bond        0.00094 (    1)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.7484 (m110) cc_final: 0.6895 (t0)
REVERT: A   82 PHE cc_start: 0.6672 (OUTLIER) cc_final: 0.5833 (p90)
  outliers start: 9
  outliers final: 2
  residues processed: 41
  average time/residue: 0.2891
  time to fit residues: 12.7670
Evaluate side-chains
  38 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 35
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 PHE
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  297 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0980
   chunk 9 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 23 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.132639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.119784 restraints weight = 4871.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 1.36
r_work: 0.3272 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4127  Z= 0.123
  Angle     :  0.537   6.028   5623  Z= 0.265
  Chirality :  0.045   0.363    635
  Planarity :  0.004   0.037    703
  Dihedral  : 11.050 111.866    614
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 11.19 %
    Favored  : 87.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.39), residues: 506
  helix:  1.23 (0.34), residues: 262
  sheet: -0.23 (0.64), residues: 56
  loop : -0.74 (0.47), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 193 
 TYR   0.007   0.001   TYR A 104 
 PHE   0.010   0.001   PHE A 174 
 TRP   0.009   0.001   TRP A 489 
 HIS   0.001   0.000   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4126)
  covalent geometry    : angle       0.53700 ( 5623)
  hydrogen bonds       : bond        0.03285 (  205)
  hydrogen bonds       : angle       4.70362 (  558)
  Misc. bond           : bond        0.00103 (    1)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.093 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.7492 (m110) cc_final: 0.6891 (t0)
REVERT: A   82 PHE cc_start: 0.6666 (OUTLIER) cc_final: 0.5834 (p90)
  outliers start: 6
  outliers final: 2
  residues processed: 39
  average time/residue: 0.2960
  time to fit residues: 12.3154
Evaluate side-chains
  37 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 PHE
Chi-restraints excluded: chain A residue  287 GLU
Chi-restraints excluded: chain A residue  297 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 8 optimal weight:    0.1980
   chunk 20 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 4 optimal weight:    0.4980
   chunk 10 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.133951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.120987 restraints weight = 4856.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 1.37
r_work: 0.3305 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4127  Z= 0.106
  Angle     :  0.523   6.080   5623  Z= 0.258
  Chirality :  0.044   0.324    635
  Planarity :  0.004   0.037    703
  Dihedral  : 10.906 111.105    614
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 11.44 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.38), residues: 506
  helix:  1.30 (0.34), residues: 259
  sheet: -0.18 (0.65), residues: 56
  loop : -0.76 (0.46), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 193 
 TYR   0.006   0.001   TYR A 406 
 PHE   0.009   0.001   PHE A  28 
 TRP   0.010   0.001   TRP A 489 
 HIS   0.001   0.000   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 4126)
  covalent geometry    : angle       0.52334 ( 5623)
  hydrogen bonds       : bond        0.03109 (  205)
  hydrogen bonds       : angle       4.63257 (  558)
  Misc. bond           : bond        0.00094 (    1)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.7489 (m110) cc_final: 0.6907 (t0)
REVERT: A   82 PHE cc_start: 0.6719 (OUTLIER) cc_final: 0.5939 (p90)
  outliers start: 6
  outliers final: 1
  residues processed: 41
  average time/residue: 0.2870
  time to fit residues: 12.6506
Evaluate side-chains
  35 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 PHE
Chi-restraints excluded: chain A residue  297 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0030
   chunk 36 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.6390

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.133108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.120175 restraints weight = 4777.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 1.34
r_work: 0.3279 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.3182 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4127  Z= 0.117
  Angle     :  0.533   6.223   5623  Z= 0.262
  Chirality :  0.044   0.302    635
  Planarity :  0.004   0.037    703
  Dihedral  : 10.832 110.465    614
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 12.41 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.38), residues: 506
  helix:  1.27 (0.34), residues: 259
  sheet: -0.20 (0.65), residues: 56
  loop : -0.72 (0.45), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 193 
 TYR   0.007   0.001   TYR A 104 
 PHE   0.010   0.001   PHE A 174 
 TRP   0.009   0.001   TRP A 489 
 HIS   0.001   0.000   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 4126)
  covalent geometry    : angle       0.53250 ( 5623)
  hydrogen bonds       : bond        0.03209 (  205)
  hydrogen bonds       : angle       4.65041 (  558)
  Misc. bond           : bond        0.00096 (    1)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.7477 (m110) cc_final: 0.6911 (t0)
REVERT: A   82 PHE cc_start: 0.6714 (OUTLIER) cc_final: 0.5940 (p90)
REVERT: A  173 ASN cc_start: 0.7835 (p0) cc_final: 0.7614 (p0)
  outliers start: 5
  outliers final: 1
  residues processed: 39
  average time/residue: 0.2987
  time to fit residues: 12.5452
Evaluate side-chains
  37 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 PHE
Chi-restraints excluded: chain A residue  297 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 29 optimal weight:    0.2980
   chunk 1 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.132249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.119273 restraints weight = 4929.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 1.37
r_work: 0.3267 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4127  Z= 0.133
  Angle     :  0.546   6.363   5623  Z= 0.270
  Chirality :  0.045   0.299    635
  Planarity :  0.004   0.036    703
  Dihedral  : 10.831 110.014    614
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 12.65 %
    Favored  : 86.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.39), residues: 506
  helix:  1.24 (0.34), residues: 262
  sheet: -0.21 (0.65), residues: 56
  loop : -0.65 (0.47), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 193 
 TYR   0.007   0.001   TYR A 104 
 PHE   0.011   0.001   PHE A 174 
 TRP   0.009   0.001   TRP A 489 
 HIS   0.001   0.001   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 4126)
  covalent geometry    : angle       0.54594 ( 5623)
  hydrogen bonds       : bond        0.03339 (  205)
  hydrogen bonds       : angle       4.69784 (  558)
  Misc. bond           : bond        0.00093 (    1)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.7486 (m110) cc_final: 0.6864 (t0)
REVERT: A   82 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.5824 (p90)
REVERT: A  173 ASN cc_start: 0.7767 (p0) cc_final: 0.7561 (p0)
  outliers start: 3
  outliers final: 1
  residues processed: 38
  average time/residue: 0.2862
  time to fit residues: 11.7061
Evaluate side-chains
  38 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 PHE
Chi-restraints excluded: chain A residue  297 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 45 optimal weight:    0.3980
   chunk 21 optimal weight:    0.4980
   chunk 1 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.133515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.120565 restraints weight = 4814.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.35
r_work: 0.3282 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4127  Z= 0.112
  Angle     :  0.530   6.423   5623  Z= 0.262
  Chirality :  0.044   0.290    635
  Planarity :  0.004   0.037    703
  Dihedral  : 10.698 108.583    614
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 13.14 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.39), residues: 506
  helix:  1.31 (0.34), residues: 262
  sheet: -0.15 (0.66), residues: 56
  loop : -0.65 (0.47), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 193 
 TYR   0.006   0.001   TYR A 325 
 PHE   0.009   0.001   PHE A 174 
 TRP   0.010   0.001   TRP A 489 
 HIS   0.001   0.000   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 4126)
  covalent geometry    : angle       0.52954 ( 5623)
  hydrogen bonds       : bond        0.03158 (  205)
  hydrogen bonds       : angle       4.59429 (  558)
  Misc. bond           : bond        0.00090 (    1)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.7473 (m110) cc_final: 0.6890 (t0)
REVERT: A   82 PHE cc_start: 0.6674 (OUTLIER) cc_final: 0.5870 (p90)
REVERT: A  173 ASN cc_start: 0.7768 (p0) cc_final: 0.7552 (p0)
  outliers start: 2
  outliers final: 1
  residues processed: 39
  average time/residue: 0.2979
  time to fit residues: 12.5137
Evaluate side-chains
  38 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 36
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 PHE
Chi-restraints excluded: chain A residue  297 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.130933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.117939 restraints weight = 4912.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 1.36
r_work: 0.3261 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 3.11 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4127  Z= 0.132
  Angle     :  0.544   6.323   5623  Z= 0.269
  Chirality :  0.044   0.285    635
  Planarity :  0.005   0.036    703
  Dihedral  : 10.726 109.043    614
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 13.14 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.39), residues: 506
  helix:  1.25 (0.34), residues: 262
  sheet: -0.20 (0.66), residues: 56
  loop : -0.66 (0.47), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 193 
 TYR   0.007   0.001   TYR A 104 
 PHE   0.011   0.001   PHE A 174 
 TRP   0.009   0.001   TRP A 489 
 HIS   0.001   0.001   HIS A 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 4126)
  covalent geometry    : angle       0.54405 ( 5623)
  hydrogen bonds       : bond        0.03349 (  205)
  hydrogen bonds       : angle       4.65244 (  558)
  Misc. bond           : bond        0.00095 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1236.39 seconds
wall clock time: 21 minutes 51.79 seconds (1311.79 seconds total)