Starting phenix.real_space_refine
on Wed Sep 17 06:07:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kml_62437/09_2025/9kml_62437.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kml_62437/09_2025/9kml_62437.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kml_62437/09_2025/9kml_62437.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kml_62437/09_2025/9kml_62437.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kml_62437/09_2025/9kml_62437.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kml_62437/09_2025/9kml_62437.map"
  }
  resolution = 3.11
  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=  -0.000 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     Cl      1      4.86       5
     C    3854      2.51       5
     N     931      2.21       5
     O    1045      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5872
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 922
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 2, 'TRANS': 115}
    Chain: "A"
      Number of atoms: 4145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 520, 4145
          Classifications: {'peptide': 520}
          Link IDs: {'PTRANS': 25, 'TRANS': 494}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 804
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.72, per 1000 atoms: 0.29
  Number of scatterers: 5872
  At special positions: 0
  Unit cell: (72.16, 82.82, 113.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      41     16.00
     O    1045      8.00
     N     931      7.00
     C    3854      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 171 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03

  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: 0.52
  Conformation dependent library (CDL) restraints added in 170.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1352

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 7 sheets defined
      54.3% alpha, 13.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.587A  pdb=" N   SER H  31 " --> pdb=" O   THR H  28 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 28 through 32'
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.852A  pdb=" N   ASP H  90 " --> pdb=" O   ARG H  87 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 87 through 91'
    Processing helix  chain 'A' and resid 60 through 65
    Processing helix  chain 'A' and resid 65 through 74
      removed outlier: 3.772A  pdb=" N   TYR A  69 " --> pdb=" O   TRP A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 79 through 90
    Processing helix  chain 'A' and resid 90 through 105
    Processing helix  chain 'A' and resid 117 through 120
    Processing helix  chain 'A' and resid 121 through 151
      removed outlier: 4.184A  pdb=" N   TYR A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 177
    Processing helix  chain 'A' and resid 193 through 203
    Processing helix  chain 'A' and resid 219 through 236
      removed outlier: 4.328A  pdb=" N   TRP A 236 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 266
      removed outlier: 3.739A  pdb=" N   THR A 266 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 279
      removed outlier: 4.170A  pdb=" N   GLY A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 286
      removed outlier: 3.551A  pdb=" N   GLY A 286 " --> pdb=" O   SER A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 302
      removed outlier: 4.293A  pdb=" N   TRP A 291 " --> pdb=" O   ASP A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 315
      removed outlier: 3.574A  pdb=" N   TYR A 315 " --> pdb=" O   SER A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 356
    Processing helix  chain 'A' and resid 358 through 362
      removed outlier: 3.653A  pdb=" N   VAL A 362 " --> pdb=" O   ILE A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 380
    Processing helix  chain 'A' and resid 383 through 418
      removed outlier: 3.666A  pdb=" N   TRP A 387 " --> pdb=" O   LEU A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 444
    Processing helix  chain 'A' and resid 450 through 462
      removed outlier: 3.939A  pdb=" N   VAL A 454 " --> pdb=" O   GLY A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 482
    Processing helix  chain 'A' and resid 484 through 496
    Processing helix  chain 'A' and resid 501 through 510
    Processing helix  chain 'A' and resid 510 through 526
      removed outlier: 3.612A  pdb=" N   LEU A 524 " --> pdb=" O   PHE A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 555
      removed outlier: 3.835A  pdb=" N   SER A 553 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 567
    Processing helix  chain 'A' and resid 571 through 581
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 3.940A  pdb=" N   ALA L  84 " --> pdb=" O   ALA L  81 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5
      removed outlier: 3.566A  pdb=" N   SER H  71 " --> pdb=" O   HIS H  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.859A  pdb=" N   THR H 113 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   SER H  40 " --> pdb=" O   LEU H  45 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   LEU H  45 " --> pdb=" O   SER H  40 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.859A  pdb=" N   THR H 113 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   TYR H 108 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 531 through 532
    Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6
      removed outlier: 12.362A  pdb=" N   CYS L  23 " --> pdb=" O   THR L  75 " (cutoff:3.500A)
      removed outlier: 11.583A  pdb=" N   THR L  75 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
      removed outlier: 12.000A  pdb=" N   ALA L  25 " --> pdb=" O   SER L  73 " (cutoff:3.500A)
      removed outlier: 11.785A  pdb=" N   SER L  73 " --> pdb=" O   ALA L  25 " (cutoff:3.500A)
      removed outlier: 11.616A  pdb=" N   SER L  27 " --> pdb=" O   SER L  71 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   SER L  71 " --> pdb=" O   SER L  27 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY L  69 " --> pdb=" O   VAL L  29 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.469A  pdb=" N   MET L  11 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'L' and resid 54 through 55
      removed outlier: 5.793A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 5.734A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    320 hydrogen bonds defined for protein.
    915 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: 0.99

  Time building geometry restraints manager: 0.64 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: 1741
        1.34 -     1.46: 1385
        1.46 -     1.58: 2855
        1.58 -     1.69: 0
        1.69 -     1.81: 60
  Bond restraints: 6041
  Sorted by residual:
  bond pdb=" CB  ILE A 141 "
       pdb=" CG1 ILE A 141 "
    ideal  model  delta    sigma   weight residual
    1.530  1.496  0.034 2.00e-02 2.50e+03 2.91e+00
  bond pdb=" CB  VAL A 140 "
       pdb=" CG1 VAL A 140 "
    ideal  model  delta    sigma   weight residual
    1.521  1.466  0.055 3.30e-02 9.18e+02 2.79e+00
  bond pdb=" N   ASN A 190 "
       pdb=" CA  ASN A 190 "
    ideal  model  delta    sigma   weight residual
    1.457  1.478 -0.021 1.29e-02 6.01e+03 2.65e+00
  bond pdb=" C   THR A 512 "
       pdb=" N   PRO A 513 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.021 1.36e-02 5.41e+03 2.41e+00
  bond pdb=" CA  PHE A  58 "
       pdb=" CB  PHE A  58 "
    ideal  model  delta    sigma   weight residual
    1.526  1.501  0.026 1.76e-02 3.23e+03 2.10e+00
  ... (remaining 6036 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 7948
        2.23 -     4.46: 228
        4.46 -     6.69: 28
        6.69 -     8.92: 8
        8.92 -    11.15: 1
  Bond angle restraints: 8213
  Sorted by residual:
  angle pdb=" C   SER L  51 "
        pdb=" N   THR L  52 "
        pdb=" CA  THR L  52 "
      ideal   model   delta    sigma   weight residual
     121.54  132.69  -11.15 1.91e+00 2.74e-01 3.41e+01
  angle pdb=" C   TRP A 218 "
        pdb=" N   ASP A 219 "
        pdb=" CA  ASP A 219 "
      ideal   model   delta    sigma   weight residual
     121.54  130.37   -8.83 1.91e+00 2.74e-01 2.14e+01
  angle pdb=" C   PHE A  58 "
        pdb=" N   VAL A  59 "
        pdb=" CA  VAL A  59 "
      ideal   model   delta    sigma   weight residual
     121.97  129.62   -7.65 1.80e+00 3.09e-01 1.81e+01
  angle pdb=" C   VAL A 136 "
        pdb=" N   TYR A 137 "
        pdb=" CA  TYR A 137 "
      ideal   model   delta    sigma   weight residual
     121.14  114.51    6.63 1.75e+00 3.27e-01 1.43e+01
  angle pdb=" C   ILE A 139 "
        pdb=" N   VAL A 140 "
        pdb=" CA  VAL A 140 "
      ideal   model   delta    sigma   weight residual
     120.64  115.00    5.64 1.64e+00 3.72e-01 1.18e+01
  ... (remaining 8208 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.21: 3096
       17.21 -    34.42: 304
       34.42 -    51.63: 49
       51.63 -    68.84: 8
       68.84 -    86.05: 6
  Dihedral angle restraints: 3463
    sinusoidal: 1323
      harmonic: 2140
  Sorted by residual:
  dihedral pdb=" CB  CYS A 162 "
           pdb=" SG  CYS A 162 "
           pdb=" SG  CYS A 171 "
           pdb=" CB  CYS A 171 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -167.10   81.10     1      1.00e+01 1.00e-02 8.12e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   51.16   41.84     1      1.00e+01 1.00e-02 2.45e+01
  dihedral pdb=" CA  HIS A 161 "
           pdb=" C   HIS A 161 "
           pdb=" N   CYS A 162 "
           pdb=" CA  CYS A 162 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.35  -24.65     0      5.00e+00 4.00e-02 2.43e+01
  ... (remaining 3460 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 603
       0.045 -    0.090: 210
       0.090 -    0.135: 69
       0.135 -    0.180: 12
       0.180 -    0.224: 5
  Chirality restraints: 899
  Sorted by residual:
  chirality pdb=" CB  THR H  28 "
            pdb=" CA  THR H  28 "
            pdb=" OG1 THR H  28 "
            pdb=" CG2 THR H  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CB  VAL A 357 "
            pdb=" CA  VAL A 357 "
            pdb=" CG1 VAL A 357 "
            pdb=" CG2 VAL A 357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CB  VAL A 140 "
            pdb=" CA  VAL A 140 "
            pdb=" CG1 VAL A 140 "
            pdb=" CG2 VAL A 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 896 not shown)

  Planarity restraints: 1013
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  92 "   -0.054 5.00e-02 4.00e+02   8.17e-02 1.07e+01
        pdb=" N   PRO A  93 "    0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO A  93 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A  93 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 219 "   -0.015 2.00e-02 2.50e+03   2.92e-02 8.55e+00
        pdb=" C   ASP A 219 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ASP A 219 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LEU A 220 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 479 "   -0.013 2.00e-02 2.50e+03   2.63e-02 6.91e+00
        pdb=" C   ILE A 479 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ILE A 479 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ALA A 480 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1010 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1119
        2.77 -     3.30: 5491
        3.30 -     3.83: 10597
        3.83 -     4.37: 12248
        4.37 -     4.90: 21481
  Nonbonded interactions: 50936
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  69 "
            pdb=" OD2 ASP A 459 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   LYS A 376 "
            pdb=" OG1 THR A 379 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OD1 ASP A 174 "
            pdb=" OG  SER A 193 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" OH  TYR A  72 "
            pdb=" O   ILE A 359 "
     model   vdw
     2.359 3.040
  nonbonded pdb=" NH1 ARG H  67 "
            pdb=" OD2 ASP H  90 "
     model   vdw
     2.364 3.120
  ... (remaining 50931 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:                  0.010
  Normalize map: mean=0, sd=1:             4.610
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.300
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
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      :  0.006   0.062   6044  Z= 0.253
  Angle     :  0.884  11.151   8219  Z= 0.488
  Chirality :  0.053   0.224    899
  Planarity :  0.008   0.082   1013
  Dihedral  : 13.751  86.049   2102
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.16 %
    Favored  : 99.68 %
  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: -1.86 (0.28), residues: 738
  helix: -0.90 (0.24), residues: 352
  sheet: -1.22 (0.51), residues: 108
  loop : -1.46 (0.36), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 201 
 TYR   0.029   0.002   TYR H  57 
 PHE   0.031   0.003   PHE L  92 
 TRP   0.015   0.002   TRP A  65 
 HIS   0.006   0.002   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00587 ( 6041)
  covalent geometry    : angle       0.88356 ( 8213)
  SS BOND              : bond        0.00189 (    3)
  SS BOND              : angle       1.22339 (    6)
  hydrogen bonds       : bond        0.15836 (  316)
  hydrogen bonds       : angle       7.35374 (  915)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.251 
Fit side-chains
REVERT: H   57 TYR cc_start: 0.8511 (m-80) cc_final: 0.7904 (m-80)
REVERT: A   72 TYR cc_start: 0.8511 (t80) cc_final: 0.8076 (t80)
REVERT: A  191 PHE cc_start: 0.7389 (m-80) cc_final: 0.7168 (m-80)
REVERT: A  258 LEU cc_start: 0.7975 (tp) cc_final: 0.7732 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 124
  average time/residue: 0.0991
  time to fit residues: 15.7457
Evaluate side-chains
  95 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3796 r_free = 0.3796 target = 0.160438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.132020 restraints weight = 7035.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.85
r_work: 0.3329 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6044  Z= 0.203
  Angle     :  0.621   8.503   8219  Z= 0.333
  Chirality :  0.043   0.159    899
  Planarity :  0.006   0.070   1013
  Dihedral  :  5.044  19.746    819
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  9.02 %
    Favored  : 89.24 %
  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: -0.98 (0.30), residues: 738
  helix:  0.17 (0.26), residues: 359
  sheet: -1.54 (0.48), residues: 117
  loop : -1.19 (0.38), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 240 
 TYR   0.018   0.002   TYR A 137 
 PHE   0.020   0.002   PHE A 455 
 TRP   0.030   0.002   TRP A 218 
 HIS   0.003   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 6041)
  covalent geometry    : angle       0.62128 ( 8213)
  SS BOND              : bond        0.00266 (    3)
  SS BOND              : angle       0.84310 (    6)
  hydrogen bonds       : bond        0.04838 (  316)
  hydrogen bonds       : angle       5.48458 (  915)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.242 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.8774 (tt0) cc_final: 0.8373 (tt0)
REVERT: H   57 TYR cc_start: 0.8920 (m-80) cc_final: 0.8523 (m-80)
REVERT: H   78 ILE cc_start: 0.8132 (mp) cc_final: 0.7859 (mp)
REVERT: A  191 PHE cc_start: 0.7615 (m-80) cc_final: 0.7259 (m-80)
REVERT: A  440 TYR cc_start: 0.8159 (t80) cc_final: 0.7957 (t80)
  outliers start: 11
  outliers final: 9
  residues processed: 111
  average time/residue: 0.0910
  time to fit residues: 13.2331
Evaluate side-chains
  109 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue   97 LEU
Chi-restraints excluded: chain L residue  105 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 17 optimal weight:    0.0980
   chunk 64 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 71 optimal weight:    0.3980
   chunk 12 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 59 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   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  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.159323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.130758 restraints weight = 6907.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 1.91
r_work: 0.3360 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6044  Z= 0.151
  Angle     :  0.562   7.279   8219  Z= 0.299
  Chirality :  0.041   0.163    899
  Planarity :  0.005   0.064   1013
  Dihedral  :  4.728  18.358    819
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 12.34 %
    Favored  : 85.92 %
  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: -0.44 (0.31), residues: 738
  helix:  0.71 (0.26), residues: 359
  sheet: -1.35 (0.49), residues: 112
  loop : -1.08 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 240 
 TYR   0.022   0.001   TYR A 137 
 PHE   0.016   0.002   PHE A 473 
 TRP   0.020   0.001   TRP A 470 
 HIS   0.002   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6041)
  covalent geometry    : angle       0.56149 ( 8213)
  SS BOND              : bond        0.00212 (    3)
  SS BOND              : angle       0.58397 (    6)
  hydrogen bonds       : bond        0.04435 (  316)
  hydrogen bonds       : angle       5.17210 (  915)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.230 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.8817 (tt0) cc_final: 0.8290 (tt0)
REVERT: H   57 TYR cc_start: 0.8952 (m-80) cc_final: 0.8451 (m-80)
REVERT: H   78 ILE cc_start: 0.7870 (mp) cc_final: 0.7563 (mp)
REVERT: A  191 PHE cc_start: 0.7605 (m-80) cc_final: 0.7243 (m-80)
  outliers start: 11
  outliers final: 9
  residues processed: 117
  average time/residue: 0.0913
  time to fit residues: 13.8873
Evaluate side-chains
  111 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   97 LEU
Chi-restraints excluded: chain L residue  105 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0670
   chunk 34 optimal weight:    0.0970
   chunk 29 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 41 optimal weight:    0.2980
   chunk 28 optimal weight:    0.9980
   chunk 65 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.4316

-------------------------------------------------------------------------------
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 = 0.3798 r_free = 0.3798 target = 0.159825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.130521 restraints weight = 6976.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.03
r_work: 0.3338 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6044  Z= 0.141
  Angle     :  0.547   8.791   8219  Z= 0.291
  Chirality :  0.041   0.171    899
  Planarity :  0.005   0.060   1013
  Dihedral  :  4.552  17.866    819
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 14.08 %
    Favored  : 83.39 %
  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: -0.09 (0.31), residues: 738
  helix:  0.96 (0.27), residues: 359
  sheet: -0.99 (0.52), residues: 101
  loop : -0.96 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  44 
 TYR   0.022   0.001   TYR A 137 
 PHE   0.015   0.001   PHE A 455 
 TRP   0.027   0.001   TRP A 218 
 HIS   0.002   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6041)
  covalent geometry    : angle       0.54702 ( 8213)
  SS BOND              : bond        0.00155 (    3)
  SS BOND              : angle       0.52178 (    6)
  hydrogen bonds       : bond        0.04191 (  316)
  hydrogen bonds       : angle       5.01793 (  915)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.228 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.8827 (tt0) cc_final: 0.8239 (tt0)
REVERT: H   57 TYR cc_start: 0.8968 (m-80) cc_final: 0.8465 (m-80)
REVERT: H   78 ILE cc_start: 0.7932 (mp) cc_final: 0.7602 (mp)
REVERT: A  155 LYS cc_start: 0.8458 (tttp) cc_final: 0.7366 (mmtt)
REVERT: A  191 PHE cc_start: 0.7672 (m-80) cc_final: 0.7238 (m-80)
REVERT: A  440 TYR cc_start: 0.8244 (t80) cc_final: 0.7761 (t80)
REVERT: L   17 GLU cc_start: 0.6477 (tm-30) cc_final: 0.6242 (tm-30)
  outliers start: 16
  outliers final: 12
  residues processed: 115
  average time/residue: 0.0904
  time to fit residues: 13.6453
Evaluate side-chains
  110 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  105 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 36 optimal weight:    0.2980
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3764 r_free = 0.3764 target = 0.156730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.127624 restraints weight = 7110.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 1.96
r_work: 0.3305 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6044  Z= 0.178
  Angle     :  0.572   8.005   8219  Z= 0.304
  Chirality :  0.042   0.169    899
  Planarity :  0.005   0.061   1013
  Dihedral  :  4.583  17.904    819
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 14.08 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.10 (0.31), residues: 738
  helix:  1.02 (0.27), residues: 359
  sheet: -1.32 (0.49), residues: 112
  loop : -0.87 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 201 
 TYR   0.021   0.001   TYR A 137 
 PHE   0.015   0.002   PHE A 455 
 TRP   0.018   0.001   TRP A 470 
 HIS   0.002   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 6041)
  covalent geometry    : angle       0.57202 ( 8213)
  SS BOND              : bond        0.00359 (    3)
  SS BOND              : angle       0.90308 (    6)
  hydrogen bonds       : bond        0.04407 (  316)
  hydrogen bonds       : angle       5.03071 (  915)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.232 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.8851 (tt0) cc_final: 0.8314 (tt0)
REVERT: H   57 TYR cc_start: 0.8984 (m-80) cc_final: 0.8518 (m-80)
REVERT: H   78 ILE cc_start: 0.7995 (mp) cc_final: 0.7644 (mp)
REVERT: A  155 LYS cc_start: 0.8492 (tttp) cc_final: 0.7442 (mmtt)
REVERT: A  191 PHE cc_start: 0.7681 (m-80) cc_final: 0.7399 (m-10)
REVERT: A  440 TYR cc_start: 0.8428 (t80) cc_final: 0.7847 (t80)
  outliers start: 21
  outliers final: 17
  residues processed: 111
  average time/residue: 0.0846
  time to fit residues: 12.2191
Evaluate side-chains
  117 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  105 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0170
   chunk 19 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 29 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 22 optimal weight:    0.3980
   chunk 35 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
H  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.157270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.128666 restraints weight = 7018.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 1.94
r_work: 0.3303 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6044  Z= 0.155
  Angle     :  0.555   8.534   8219  Z= 0.294
  Chirality :  0.041   0.170    899
  Planarity :  0.005   0.059   1013
  Dihedral  :  4.484  17.349    819
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 15.03 %
    Favored  : 81.65 %
  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:  0.09 (0.31), residues: 738
  helix:  1.10 (0.27), residues: 359
  sheet: -0.99 (0.52), residues: 106
  loop : -0.81 (0.39), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 201 
 TYR   0.022   0.001   TYR A 137 
 PHE   0.013   0.002   PHE A 455 
 TRP   0.018   0.001   TRP A 470 
 HIS   0.002   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 6041)
  covalent geometry    : angle       0.55485 ( 8213)
  SS BOND              : bond        0.00313 (    3)
  SS BOND              : angle       0.64975 (    6)
  hydrogen bonds       : bond        0.04220 (  316)
  hydrogen bonds       : angle       4.95880 (  915)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.233 
Fit side-chains
REVERT: H   46 GLU cc_start: 0.8862 (tt0) cc_final: 0.8329 (tt0)
REVERT: H   57 TYR cc_start: 0.8980 (m-80) cc_final: 0.8521 (m-80)
REVERT: H   78 ILE cc_start: 0.7995 (mp) cc_final: 0.7648 (mp)
REVERT: A  155 LYS cc_start: 0.8486 (tttp) cc_final: 0.7428 (mmtt)
REVERT: A  191 PHE cc_start: 0.7637 (m-80) cc_final: 0.7349 (m-10)
REVERT: A  304 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6084 (tp)
REVERT: A  322 SER cc_start: 0.8382 (m) cc_final: 0.8091 (p)
REVERT: A  440 TYR cc_start: 0.8449 (t80) cc_final: 0.7873 (t80)
  outliers start: 21
  outliers final: 16
  residues processed: 117
  average time/residue: 0.0823
  time to fit residues: 12.8239
Evaluate side-chains
  118 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue  105 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 36 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9980
   chunk 58 optimal weight:    0.1980
   chunk 38 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
H  77 ASN

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 = 0.154719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.125775 restraints weight = 7094.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 1.95
r_work: 0.3287 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6044  Z= 0.193
  Angle     :  0.588   7.929   8219  Z= 0.312
  Chirality :  0.043   0.171    899
  Planarity :  0.005   0.059   1013
  Dihedral  :  4.557  18.115    819
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.51 %
    Favored  : 81.49 %
  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: -0.02 (0.31), residues: 738
  helix:  1.04 (0.27), residues: 359
  sheet: -1.23 (0.50), residues: 112
  loop : -0.81 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  44 
 TYR   0.022   0.002   TYR A 137 
 PHE   0.017   0.002   PHE A 455 
 TRP   0.017   0.001   TRP A 470 
 HIS   0.002   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 6041)
  covalent geometry    : angle       0.58796 ( 8213)
  SS BOND              : bond        0.00182 (    3)
  SS BOND              : angle       0.75236 (    6)
  hydrogen bonds       : bond        0.04485 (  316)
  hydrogen bonds       : angle       5.03458 (  915)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.8871 (tt0) cc_final: 0.8329 (tt0)
REVERT: H   57 TYR cc_start: 0.8989 (m-80) cc_final: 0.8582 (m-80)
REVERT: H   78 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7574 (mp)
REVERT: A  155 LYS cc_start: 0.8492 (tttp) cc_final: 0.7430 (mmtt)
REVERT: A  191 PHE cc_start: 0.7693 (m-80) cc_final: 0.7338 (m-80)
REVERT: A  304 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6470 (tp)
REVERT: A  322 SER cc_start: 0.8482 (m) cc_final: 0.8148 (p)
  outliers start: 19
  outliers final: 15
  residues processed: 115
  average time/residue: 0.0891
  time to fit residues: 13.4073
Evaluate side-chains
  122 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue   78 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   77 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 14 optimal weight:    0.4980
   chunk 23 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3775 r_free = 0.3775 target = 0.156421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.124932 restraints weight = 6965.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 2.23
r_work: 0.3300 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6044  Z= 0.174
  Angle     :  0.573   8.009   8219  Z= 0.304
  Chirality :  0.042   0.172    899
  Planarity :  0.005   0.058   1013
  Dihedral  :  4.526  17.983    819
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.35 %
    Favored  : 81.65 %
  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:  0.02 (0.32), residues: 738
  helix:  1.08 (0.27), residues: 359
  sheet: -1.21 (0.50), residues: 112
  loop : -0.78 (0.40), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  44 
 TYR   0.022   0.001   TYR A 137 
 PHE   0.014   0.002   PHE A 455 
 TRP   0.024   0.001   TRP A 218 
 HIS   0.002   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 6041)
  covalent geometry    : angle       0.57309 ( 8213)
  SS BOND              : bond        0.00179 (    3)
  SS BOND              : angle       0.64387 (    6)
  hydrogen bonds       : bond        0.04329 (  316)
  hydrogen bonds       : angle       5.00935 (  915)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.8896 (tt0) cc_final: 0.8363 (tt0)
REVERT: H   57 TYR cc_start: 0.8984 (m-80) cc_final: 0.8573 (m-80)
REVERT: H   78 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7496 (mp)
REVERT: A  155 LYS cc_start: 0.8493 (tttp) cc_final: 0.7419 (mmtt)
REVERT: A  191 PHE cc_start: 0.7753 (m-80) cc_final: 0.7363 (m-80)
REVERT: A  304 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.6436 (tp)
REVERT: A  322 SER cc_start: 0.8357 (m) cc_final: 0.8024 (p)
  outliers start: 19
  outliers final: 14
  residues processed: 115
  average time/residue: 0.0813
  time to fit residues: 12.1472
Evaluate side-chains
  119 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue   78 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain L residue   77 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3732 r_free = 0.3732 target = 0.154233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.124683 restraints weight = 7083.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 2.04
r_work: 0.3247 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6044  Z= 0.194
  Angle     :  0.589   8.004   8219  Z= 0.312
  Chirality :  0.042   0.170    899
  Planarity :  0.005   0.057   1013
  Dihedral  :  4.544  18.124    819
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.66 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.00 (0.31), residues: 738
  helix:  1.02 (0.27), residues: 359
  sheet: -0.96 (0.51), residues: 106
  loop : -0.87 (0.39), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  62 
 TYR   0.022   0.002   TYR A 137 
 PHE   0.015   0.002   PHE A 455 
 TRP   0.018   0.001   TRP A 470 
 HIS   0.002   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 6041)
  covalent geometry    : angle       0.58897 ( 8213)
  SS BOND              : bond        0.00178 (    3)
  SS BOND              : angle       0.69608 (    6)
  hydrogen bonds       : bond        0.04475 (  316)
  hydrogen bonds       : angle       5.05015 (  915)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.8875 (tt0) cc_final: 0.8279 (tt0)
REVERT: H   57 TYR cc_start: 0.8998 (m-80) cc_final: 0.8565 (m-80)
REVERT: H   78 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7507 (mp)
REVERT: A  155 LYS cc_start: 0.8490 (tttp) cc_final: 0.7425 (mmtt)
REVERT: A  191 PHE cc_start: 0.7824 (m-80) cc_final: 0.7438 (m-80)
REVERT: A  225 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7781 (tt)
REVERT: A  304 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6364 (tp)
REVERT: A  322 SER cc_start: 0.8375 (m) cc_final: 0.8017 (p)
  outliers start: 19
  outliers final: 15
  residues processed: 116
  average time/residue: 0.0866
  time to fit residues: 13.2080
Evaluate side-chains
  122 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue   78 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   77 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 63 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 19 optimal weight:    0.3980
   chunk 23 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3736 r_free = 0.3736 target = 0.154625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.125114 restraints weight = 7010.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 2.04
r_work: 0.3268 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6044  Z= 0.184
  Angle     :  0.582   7.876   8219  Z= 0.308
  Chirality :  0.042   0.171    899
  Planarity :  0.005   0.057   1013
  Dihedral  :  4.519  18.036    819
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 15.82 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.04 (0.31), residues: 738
  helix:  1.06 (0.27), residues: 358
  sheet: -1.00 (0.51), residues: 106
  loop : -0.83 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  44 
 TYR   0.022   0.001   TYR A 137 
 PHE   0.014   0.002   PHE A 455 
 TRP   0.018   0.001   TRP A 470 
 HIS   0.002   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 6041)
  covalent geometry    : angle       0.58144 ( 8213)
  SS BOND              : bond        0.00209 (    3)
  SS BOND              : angle       0.66481 (    6)
  hydrogen bonds       : bond        0.04395 (  316)
  hydrogen bonds       : angle       5.02523 (  915)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.8852 (tt0) cc_final: 0.8265 (tt0)
REVERT: H   57 TYR cc_start: 0.8992 (m-80) cc_final: 0.8564 (m-80)
REVERT: H   78 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7533 (mp)
REVERT: A  155 LYS cc_start: 0.8491 (tttp) cc_final: 0.7427 (mmtt)
REVERT: A  191 PHE cc_start: 0.7849 (m-80) cc_final: 0.7454 (m-80)
REVERT: A  225 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7787 (tt)
REVERT: A  304 ILE cc_start: 0.7147 (OUTLIER) cc_final: 0.6286 (tp)
REVERT: A  322 SER cc_start: 0.8318 (m) cc_final: 0.7979 (p)
  outliers start: 18
  outliers final: 15
  residues processed: 115
  average time/residue: 0.0859
  time to fit residues: 13.1770
Evaluate side-chains
  122 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   53 SER
Chi-restraints excluded: chain H residue   78 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  112 CYS
Chi-restraints excluded: chain A residue  161 HIS
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  282 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   34 LEU
Chi-restraints excluded: chain L residue   77 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0870
   chunk 37 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0370
   chunk 31 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0770
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.3194

-------------------------------------------------------------------------------
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 = 0.3786 r_free = 0.3786 target = 0.159093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.131194 restraints weight = 6919.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 1.88
r_work: 0.3345 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6044  Z= 0.124
  Angle     :  0.544   7.557   8219  Z= 0.288
  Chirality :  0.041   0.177    899
  Planarity :  0.005   0.054   1013
  Dihedral  :  4.376  17.350    819
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 16.77 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.26 (0.32), residues: 738
  helix:  1.27 (0.27), residues: 358
  sheet: -0.88 (0.51), residues: 106
  loop : -0.76 (0.40), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  44 
 TYR   0.024   0.001   TYR A 137 
 PHE   0.013   0.001   PHE A 473 
 TRP   0.023   0.001   TRP A 218 
 HIS   0.002   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6041)
  covalent geometry    : angle       0.54355 ( 8213)
  SS BOND              : bond        0.00127 (    3)
  SS BOND              : angle       0.58960 (    6)
  hydrogen bonds       : bond        0.03961 (  316)
  hydrogen bonds       : angle       4.87746 (  915)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1910.67 seconds
wall clock time: 33 minutes 33.91 seconds (2013.91 seconds total)