Starting phenix.real_space_refine
on Wed Sep 17 06:07:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kmk_62436/09_2025/9kmk_62436.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kmk_62436/09_2025/9kmk_62436.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kmk_62436/09_2025/9kmk_62436.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kmk_62436/09_2025/9kmk_62436.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kmk_62436/09_2025/9kmk_62436.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kmk_62436/09_2025/9kmk_62436.map"
  }
  resolution = 3.06
  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=   0.024
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 12 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: "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: 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: "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: 1.54, per 1000 atoms: 0.26
  Number of scatterers: 5872
  At special positions: 0
  Unit cell: (75.44, 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 L  23 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 171 " 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: 0.47
  Conformation dependent library (CDL) restraints added in 217.5 milliseconds
  
  Enol-peptide restraints added in 476.8 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:
      26 helices and 6 sheets defined
      53.4% alpha, 13.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.978A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    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 helix  chain 'A' and resid 65 through 74
      removed outlier: 3.837A  pdb=" N   TYR A  69 " --> pdb=" O   TRP A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 90
      removed outlier: 4.118A  pdb=" N   LEU A  80 " --> pdb=" O   GLY A  76 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ILE A  81 " --> pdb=" O   GLY A  77 " (cutoff:3.500A)
      Proline residue:  A  82  - end of helix
    Processing helix  chain 'A' and resid 90 through 105
      removed outlier: 3.524A  pdb=" N   THR A 105 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 113
      removed outlier: 4.313A  pdb=" N   THR A 111 " --> pdb=" O   GLY A 108 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   TRP A 113 " --> pdb=" O   ILE A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 120
    Processing helix  chain 'A' and resid 121 through 151
      removed outlier: 4.074A  pdb=" N   TYR A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 202
    Processing helix  chain 'A' and resid 217 through 236
      removed outlier: 3.982A  pdb=" N   TRP A 236 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 266
      removed outlier: 3.710A  pdb=" N   TYR A 247 " --> pdb=" O   GLY A 243 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   THR A 251 " --> pdb=" O   TYR A 247 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
    Processing helix  chain 'A' and resid 269 through 279
      removed outlier: 3.664A  pdb=" N   GLY A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 286
      removed outlier: 3.571A  pdb=" N   GLY A 286 " --> pdb=" O   SER A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 312
      removed outlier: 3.991A  pdb=" N   TRP A 291 " --> pdb=" O   ASP A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 355
      removed outlier: 3.513A  pdb=" N   CYS A 326 " --> pdb=" O   SER A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 379
    Processing helix  chain 'A' and resid 383 through 418
      removed outlier: 3.574A  pdb=" N   TRP A 387 " --> pdb=" O   LEU A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 444
      removed outlier: 3.692A  pdb=" N   ILE A 432 " --> pdb=" O   ARG A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 462
      removed outlier: 3.680A  pdb=" N   VAL A 454 " --> pdb=" O   GLY A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 482
      removed outlier: 3.778A  pdb=" N   LEU A 469 " --> pdb=" O   GLY A 465 " (cutoff:3.500A)
    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
    Processing helix  chain 'A' and resid 539 through 555
    Processing helix  chain 'A' and resid 555 through 568
    Processing helix  chain 'A' and resid 571 through 581
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.040A  pdb=" N   TYR H 108 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
      removed outlier: 5.689A  pdb=" N   CYS H  96 " --> pdb=" O   GLY H 110 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   GLY H 112 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   TYR H  94 " --> pdb=" O   GLY H 112 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   THR H 114 " --> pdb=" O   ALA H  92 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   ALA H  92 " --> pdb=" O   THR H 114 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   MET H  34 " --> pdb=" O   GLU H  50 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   GLU H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, 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=AA4, 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=AA4
    Processing sheet with id=AA5, 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)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 531 through 532

    318 hydrogen bonds defined for protein.
    921 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: 0.86

  Time building geometry restraints manager: 0.65 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: 1737
        1.34 -     1.46: 1399
        1.46 -     1.58: 2845
        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  1.493  0.037 2.00e-02 2.50e+03 3.46e+00
  bond pdb=" CB  VAL A 140 "
       pdb=" CG1 VAL A 140 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.39e+00
  bond pdb=" CG1 ILE A 292 "
       pdb=" CD1 ILE A 292 "
    ideal  model  delta    sigma   weight residual
    1.513  1.449  0.064 3.90e-02 6.57e+02 2.70e+00
  bond pdb=" SD  MET A 452 "
       pdb=" CE  MET A 452 "
    ideal  model  delta    sigma   weight residual
    1.791  1.750  0.041 2.50e-02 1.60e+03 2.69e+00
  bond pdb=" CB  VAL A  94 "
       pdb=" CG2 VAL A  94 "
    ideal  model  delta    sigma   weight residual
    1.521  1.471  0.050 3.30e-02 9.18e+02 2.27e+00
  ... (remaining 6036 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 7934
        2.23 -     4.46: 222
        4.46 -     6.69: 43
        6.69 -     8.92: 11
        8.92 -    11.15: 3
  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   LYS A 317 "
        pdb=" N   TYR A 318 "
        pdb=" CA  TYR A 318 "
      ideal   model   delta    sigma   weight residual
     120.79  127.27   -6.48 1.39e+00 5.18e-01 2.17e+01
  angle pdb=" N   GLY A  62 "
        pdb=" CA  GLY A  62 "
        pdb=" C   GLY A  62 "
      ideal   model   delta    sigma   weight residual
     113.18  103.70    9.48 2.37e+00 1.78e-01 1.60e+01
  angle pdb=" N   TYR A 318 "
        pdb=" CA  TYR A 318 "
        pdb=" C   TYR A 318 "
      ideal   model   delta    sigma   weight residual
     111.02  115.88   -4.86 1.22e+00 6.72e-01 1.59e+01
  angle pdb=" C   ARG A 427 "
        pdb=" N   ARG A 428 "
        pdb=" CA  ARG A 428 "
      ideal   model   delta    sigma   weight residual
     121.54  129.00   -7.46 1.91e+00 2.74e-01 1.52e+01
  ... (remaining 8208 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 3109
       17.40 -    34.81: 299
       34.81 -    52.21: 44
       52.21 -    69.62: 6
       69.62 -    87.02: 5
  Dihedral angle restraints: 3463
    sinusoidal: 1323
      harmonic: 2140
  Sorted by residual:
  dihedral pdb=" CA  TYR A 320 "
           pdb=" C   TYR A 320 "
           pdb=" N   ASN A 321 "
           pdb=" CA  ASN A 321 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.47   25.53     0      5.00e+00 4.00e-02 2.61e+01
  dihedral pdb=" CA  CYS A 171 "
           pdb=" C   CYS A 171 "
           pdb=" N   MET A 172 "
           pdb=" CA  MET A 172 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.92   23.08     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  TYR L  95 "
           pdb=" C   TYR L  95 "
           pdb=" N   PRO L  96 "
           pdb=" CA  PRO L  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.06   21.94     0      5.00e+00 4.00e-02 1.93e+01
  ... (remaining 3460 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 828
       0.104 -    0.208: 68
       0.208 -    0.312: 2
       0.312 -    0.417: 0
       0.417 -    0.521: 1
  Chirality restraints: 899
  Sorted by residual:
  chirality pdb=" CB  VAL A 447 "
            pdb=" CA  VAL A 447 "
            pdb=" CG1 VAL A 447 "
            pdb=" CG2 VAL A 447 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.11   -0.52 2.00e-01 2.50e+01 6.78e+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   -2.39   -0.24 2.00e-01 2.50e+01 1.45e+00
  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 1.23e+00
  ... (remaining 896 not shown)

  Planarity restraints: 1013
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A  67 "   -0.038 5.00e-02 4.00e+02   5.74e-02 5.27e+00
        pdb=" N   PRO A  68 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A  68 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A  68 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L   7 "   -0.038 5.00e-02 4.00e+02   5.74e-02 5.26e+00
        pdb=" N   PRO L   8 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO L   8 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO L   8 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER H  40 "    0.035 5.00e-02 4.00e+02   5.35e-02 4.58e+00
        pdb=" N   PRO H  41 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO H  41 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO H  41 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1010 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 1413
        2.78 -     3.31: 5450
        3.31 -     3.84: 10532
        3.84 -     4.37: 12363
        4.37 -     4.90: 21317
  Nonbonded interactions: 51075
  Sorted by model distance:
  nonbonded pdb=" O   SER H  52 "
            pdb=" NH1 ARG H  72 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" OH  TYR A  69 "
            pdb=" OD2 ASP A 459 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OG1 THR A 168 "
            pdb=" OE2 GLU A 197 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OH  TYR H  59 "
            pdb=" OD1 ASP A 494 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   SER A 464 "
            pdb=" OG  SER A 464 "
     model   vdw
     2.291 3.040
  ... (remaining 51070 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:             5.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.630
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
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      :  0.007   0.072   6044  Z= 0.278
  Angle     :  0.938  11.151   8219  Z= 0.512
  Chirality :  0.058   0.521    899
  Planarity :  0.007   0.057   1013
  Dihedral  : 13.803  87.023   2102
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.63 %
    Favored  : 99.37 %
  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: -1.99 (0.28), residues: 738
  helix: -1.03 (0.23), residues: 367
  sheet: -0.64 (0.52), residues: 104
  loop : -1.81 (0.35), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  66 
 TYR   0.022   0.002   TYR A 318 
 PHE   0.031   0.003   PHE L  92 
 TRP   0.016   0.002   TRP A  65 
 HIS   0.003   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00669 ( 6041)
  covalent geometry    : angle       0.93681 ( 8213)
  SS BOND              : bond        0.00148 (    3)
  SS BOND              : angle       1.70254 (    6)
  hydrogen bonds       : bond        0.16568 (  318)
  hydrogen bonds       : angle       7.64460 (  921)

*********************** 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
  102 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A  140 VAL cc_start: 0.8443 (p) cc_final: 0.8127 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0774
  time to fit residues: 10.5589
Evaluate side-chains
  90 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 53 optimal weight:    0.0870
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0870
   overall best weight:    0.3336

-------------------------------------------------------------------------------
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 = 0.3995 r_free = 0.3995 target = 0.172277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.140140 restraints weight = 6561.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 2.01
r_work: 0.3497 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.1271

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= 0.133
  Angle     :  0.589   7.578   8219  Z= 0.310
  Chirality :  0.042   0.155    899
  Planarity :  0.005   0.042   1013
  Dihedral  :  4.902  23.907    819
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  6.49 %
    Favored  : 93.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.79 (0.30), residues: 738
  helix:  0.29 (0.25), residues: 376
  sheet: -1.00 (0.49), residues: 113
  loop : -1.40 (0.38), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 240 
 TYR   0.019   0.001   TYR A 137 
 PHE   0.018   0.001   PHE A 455 
 TRP   0.010   0.001   TRP A 470 
 HIS   0.002   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6041)
  covalent geometry    : angle       0.58757 ( 8213)
  SS BOND              : bond        0.00111 (    3)
  SS BOND              : angle       1.45903 (    6)
  hydrogen bonds       : bond        0.04548 (  318)
  hydrogen bonds       : angle       5.26041 (  921)

*********************** 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
  105 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A  441 LEU cc_start: 0.8509 (mp) cc_final: 0.8209 (mm)
  outliers start: 2
  outliers final: 1
  residues processed: 104
  average time/residue: 0.0993
  time to fit residues: 13.0333
Evaluate side-chains
  89 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 17 optimal weight:    0.0060
   chunk 64 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0070
   chunk 21 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0980
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.3414

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 103 GLN
A 333 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.177719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.146013 restraints weight = 6569.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 1.91
r_work: 0.3520 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.1618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6044  Z= 0.131
  Angle     :  0.561   8.957   8219  Z= 0.295
  Chirality :  0.041   0.159    899
  Planarity :  0.004   0.040   1013
  Dihedral  :  4.546  21.090    819
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  8.23 %
    Favored  : 90.51 %
  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: -0.13 (0.31), residues: 738
  helix:  0.92 (0.26), residues: 376
  sheet: -0.84 (0.48), residues: 113
  loop : -1.17 (0.39), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  98 
 TYR   0.022   0.001   TYR A 137 
 PHE   0.018   0.001   PHE A 300 
 TRP   0.010   0.001   TRP A 218 
 HIS   0.002   0.000   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6041)
  covalent geometry    : angle       0.56003 ( 8213)
  SS BOND              : bond        0.00115 (    3)
  SS BOND              : angle       1.22059 (    6)
  hydrogen bonds       : bond        0.04221 (  318)
  hydrogen bonds       : angle       4.85309 (  921)

*********************** 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
  107 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.263 
Fit side-chains
REVERT: L   62 ARG cc_start: 0.7836 (ptt-90) cc_final: 0.7571 (ptt90)
REVERT: A  388 SER cc_start: 0.8896 (t) cc_final: 0.8312 (p)
REVERT: A  441 LEU cc_start: 0.8522 (mp) cc_final: 0.8256 (mm)
  outliers start: 8
  outliers final: 5
  residues processed: 103
  average time/residue: 0.0973
  time to fit residues: 12.9001
Evaluate side-chains
  97 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  390 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 38 optimal weight:    0.3980
   chunk 7 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0770
   chunk 18 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 22 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 46 optimal weight:    0.2980
   overall best weight:    0.3738

-------------------------------------------------------------------------------
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 = 0.4050 r_free = 0.4050 target = 0.177244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.145650 restraints weight = 6616.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 1.91
r_work: 0.3514 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3371 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6044  Z= 0.131
  Angle     :  0.550   8.172   8219  Z= 0.289
  Chirality :  0.040   0.159    899
  Planarity :  0.004   0.039   1013
  Dihedral  :  4.418  19.490    819
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  9.65 %
    Favored  : 88.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.14 (0.31), residues: 738
  helix:  1.19 (0.26), residues: 376
  sheet: -0.77 (0.48), residues: 113
  loop : -1.11 (0.39), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  98 
 TYR   0.021   0.001   TYR A 137 
 PHE   0.017   0.001   PHE A 300 
 TRP   0.010   0.001   TRP A 218 
 HIS   0.002   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6041)
  covalent geometry    : angle       0.54919 ( 8213)
  SS BOND              : bond        0.00127 (    3)
  SS BOND              : angle       1.07669 (    6)
  hydrogen bonds       : bond        0.04142 (  318)
  hydrogen bonds       : angle       4.71960 (  921)

*********************** 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
  110 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.224 
Fit side-chains
REVERT: L  107 MET cc_start: 0.8225 (mmm) cc_final: 0.7927 (mmt)
REVERT: A  138 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7631 (m-80)
REVERT: A  163 ASN cc_start: 0.7448 (t0) cc_final: 0.6967 (p0)
REVERT: A  388 SER cc_start: 0.8918 (t) cc_final: 0.8321 (p)
REVERT: A  441 LEU cc_start: 0.8515 (mp) cc_final: 0.8270 (mm)
REVERT: A  567 ARG cc_start: 0.8259 (mtm-85) cc_final: 0.7797 (mtt180)
  outliers start: 11
  outliers final: 7
  residues processed: 104
  average time/residue: 0.0907
  time to fit residues: 12.1154
Evaluate side-chains
  105 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  138 TYR
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  566 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 11 optimal weight:    0.3980
   chunk 51 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0020
   chunk 45 optimal weight:    0.9980
   chunk 66 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.5788

-------------------------------------------------------------------------------
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 = 0.4019 r_free = 0.4019 target = 0.174161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.142257 restraints weight = 6757.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 1.93
r_work: 0.3478 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6044  Z= 0.166
  Angle     :  0.574   7.304   8219  Z= 0.301
  Chirality :  0.041   0.157    899
  Planarity :  0.004   0.038   1013
  Dihedral  :  4.436  18.445    819
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 11.55 %
    Favored  : 86.39 %
  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:  0.17 (0.31), residues: 738
  helix:  1.20 (0.26), residues: 377
  sheet: -0.79 (0.47), residues: 114
  loop : -1.07 (0.40), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  98 
 TYR   0.019   0.001   TYR A 137 
 PHE   0.018   0.002   PHE A 455 
 TRP   0.011   0.001   TRP A 218 
 HIS   0.002   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 6041)
  covalent geometry    : angle       0.57342 ( 8213)
  SS BOND              : bond        0.00175 (    3)
  SS BOND              : angle       1.16404 (    6)
  hydrogen bonds       : bond        0.04356 (  318)
  hydrogen bonds       : angle       4.76374 (  921)

*********************** 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
  113 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.230 
Fit side-chains
REVERT: H   18 LEU cc_start: 0.8234 (tp) cc_final: 0.8027 (tp)
REVERT: A  212 ASN cc_start: 0.8026 (t0) cc_final: 0.7800 (t0)
REVERT: A  388 SER cc_start: 0.8943 (t) cc_final: 0.8337 (p)
REVERT: A  441 LEU cc_start: 0.8528 (mp) cc_final: 0.8269 (mm)
REVERT: A  498 TYR cc_start: 0.8951 (p90) cc_final: 0.8674 (p90)
REVERT: A  567 ARG cc_start: 0.8243 (mtm-85) cc_final: 0.7782 (mtt180)
  outliers start: 13
  outliers final: 10
  residues processed: 110
  average time/residue: 0.0917
  time to fit residues: 12.9754
Evaluate side-chains
  105 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  566 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0980
   chunk 6 optimal weight:    1.9990
   chunk 22 optimal weight:    0.2980
   chunk 35 optimal weight:    0.3980
   chunk 54 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.4028 r_free = 0.4028 target = 0.175331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.143525 restraints weight = 6677.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 1.93
r_work: 0.3487 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3338 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6044  Z= 0.147
  Angle     :  0.580  14.742   8219  Z= 0.297
  Chirality :  0.041   0.169    899
  Planarity :  0.004   0.038   1013
  Dihedral  :  4.349  17.972    819
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 12.03 %
    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:  0.25 (0.31), residues: 738
  helix:  1.29 (0.26), residues: 377
  sheet: -0.80 (0.47), residues: 114
  loop : -1.05 (0.40), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  98 
 TYR   0.020   0.001   TYR A 137 
 PHE   0.017   0.001   PHE A 300 
 TRP   0.014   0.001   TRP A 218 
 HIS   0.002   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 6041)
  covalent geometry    : angle       0.57939 ( 8213)
  SS BOND              : bond        0.00158 (    3)
  SS BOND              : angle       1.25273 (    6)
  hydrogen bonds       : bond        0.04227 (  318)
  hydrogen bonds       : angle       4.70181 (  921)

*********************** 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
  111 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.242 
Fit side-chains
REVERT: L  107 MET cc_start: 0.8283 (mmm) cc_final: 0.7997 (mmt)
REVERT: A  212 ASN cc_start: 0.7988 (t0) cc_final: 0.7762 (t0)
REVERT: A  388 SER cc_start: 0.8912 (t) cc_final: 0.8325 (p)
REVERT: A  441 LEU cc_start: 0.8496 (mp) cc_final: 0.8239 (mm)
REVERT: A  498 TYR cc_start: 0.8926 (p90) cc_final: 0.8643 (p90)
REVERT: A  567 ARG cc_start: 0.8235 (mtm-85) cc_final: 0.7783 (mtt180)
  outliers start: 13
  outliers final: 10
  residues processed: 107
  average time/residue: 0.0901
  time to fit residues: 12.3518
Evaluate side-chains
  106 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  566 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 24 optimal weight:    0.1980
   chunk 36 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0050
   chunk 40 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 10 optimal weight:    0.2980
   chunk 42 optimal weight:    0.7980
   chunk 49 optimal weight:    0.5980
   overall best weight:    0.3794

-------------------------------------------------------------------------------
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 = 0.4037 r_free = 0.4037 target = 0.176229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.144468 restraints weight = 6733.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 1.94
r_work: 0.3500 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6044  Z= 0.134
  Angle     :  0.585  16.228   8219  Z= 0.296
  Chirality :  0.041   0.168    899
  Planarity :  0.004   0.038   1013
  Dihedral  :  4.275  17.616    819
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 12.50 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.32 (0.31), residues: 738
  helix:  1.39 (0.26), residues: 377
  sheet: -0.87 (0.46), residues: 114
  loop : -1.01 (0.40), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  98 
 TYR   0.022   0.001   TYR A 137 
 PHE   0.017   0.001   PHE A 300 
 TRP   0.016   0.001   TRP A 218 
 HIS   0.004   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6041)
  covalent geometry    : angle       0.58421 ( 8213)
  SS BOND              : bond        0.00196 (    3)
  SS BOND              : angle       1.05014 (    6)
  hydrogen bonds       : bond        0.04098 (  318)
  hydrogen bonds       : angle       4.65526 (  921)

*********************** 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
  114 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.216 
Fit side-chains
REVERT: L  107 MET cc_start: 0.8298 (mmm) cc_final: 0.8007 (mmt)
REVERT: A  138 TYR cc_start: 0.7859 (OUTLIER) cc_final: 0.7533 (m-80)
REVERT: A  212 ASN cc_start: 0.7943 (t0) cc_final: 0.7722 (t0)
REVERT: A  388 SER cc_start: 0.8907 (t) cc_final: 0.8325 (p)
REVERT: A  441 LEU cc_start: 0.8484 (mp) cc_final: 0.8232 (mm)
REVERT: A  498 TYR cc_start: 0.8921 (p90) cc_final: 0.8695 (p90)
REVERT: A  567 ARG cc_start: 0.8219 (mtm-85) cc_final: 0.7773 (mtt180)
  outliers start: 14
  outliers final: 11
  residues processed: 109
  average time/residue: 0.0847
  time to fit residues: 11.8739
Evaluate side-chains
  111 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   65 THR
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  138 TYR
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  566 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 18 optimal weight:    0.2980
   chunk 53 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   chunk 58 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4012 r_free = 0.4012 target = 0.173911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.142052 restraints weight = 6731.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 1.93
r_work: 0.3478 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3322 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6044  Z= 0.170
  Angle     :  0.597  14.865   8219  Z= 0.306
  Chirality :  0.041   0.165    899
  Planarity :  0.004   0.038   1013
  Dihedral  :  4.337  17.436    819
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 13.29 %
    Favored  : 84.18 %
  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:  0.28 (0.31), residues: 738
  helix:  1.32 (0.26), residues: 377
  sheet: -0.88 (0.46), residues: 114
  loop : -0.97 (0.40), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  98 
 TYR   0.020   0.001   TYR A 137 
 PHE   0.018   0.002   PHE A 455 
 TRP   0.019   0.001   TRP A 218 
 HIS   0.004   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 6041)
  covalent geometry    : angle       0.59666 ( 8213)
  SS BOND              : bond        0.00165 (    3)
  SS BOND              : angle       1.10330 (    6)
  hydrogen bonds       : bond        0.04322 (  318)
  hydrogen bonds       : angle       4.72081 (  921)

*********************** 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
  113 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.227 
Fit side-chains
REVERT: L  107 MET cc_start: 0.8301 (mmm) cc_final: 0.8003 (mmt)
REVERT: A  212 ASN cc_start: 0.7938 (t0) cc_final: 0.7728 (t0)
REVERT: A  388 SER cc_start: 0.8920 (t) cc_final: 0.8340 (p)
REVERT: A  441 LEU cc_start: 0.8494 (mp) cc_final: 0.8235 (mm)
REVERT: A  498 TYR cc_start: 0.8934 (p90) cc_final: 0.8717 (p90)
REVERT: A  567 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.7733 (mtt180)
  outliers start: 16
  outliers final: 13
  residues processed: 107
  average time/residue: 0.0885
  time to fit residues: 12.1517
Evaluate side-chains
  109 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   65 THR
Chi-restraints excluded: chain H residue   67 ARG
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  566 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 25 optimal weight:    0.3980
   chunk 40 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   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 = 0.3998 r_free = 0.3998 target = 0.172406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.140476 restraints weight = 6755.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 1.92
r_work: 0.3456 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6044  Z= 0.182
  Angle     :  0.615  13.916   8219  Z= 0.316
  Chirality :  0.042   0.164    899
  Planarity :  0.004   0.038   1013
  Dihedral  :  4.401  17.207    819
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 13.29 %
    Favored  : 84.18 %
  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:  0.19 (0.31), residues: 738
  helix:  1.21 (0.26), residues: 377
  sheet: -0.90 (0.45), residues: 114
  loop : -0.94 (0.40), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  98 
 TYR   0.019   0.002   TYR A 137 
 PHE   0.019   0.002   PHE A 455 
 TRP   0.019   0.001   TRP A 218 
 HIS   0.004   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 6041)
  covalent geometry    : angle       0.61432 ( 8213)
  SS BOND              : bond        0.00186 (    3)
  SS BOND              : angle       1.11689 (    6)
  hydrogen bonds       : bond        0.04459 (  318)
  hydrogen bonds       : angle       4.79099 (  921)

*********************** 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
  110 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.231 
Fit side-chains
REVERT: L  107 MET cc_start: 0.8311 (mmm) cc_final: 0.8003 (mmt)
REVERT: A  212 ASN cc_start: 0.7985 (t0) cc_final: 0.7778 (t0)
REVERT: A  388 SER cc_start: 0.8950 (t) cc_final: 0.8379 (p)
REVERT: A  441 LEU cc_start: 0.8489 (mp) cc_final: 0.8231 (mm)
REVERT: A  498 TYR cc_start: 0.8926 (p90) cc_final: 0.8707 (p90)
REVERT: A  567 ARG cc_start: 0.8240 (mtm-85) cc_final: 0.7830 (mtt180)
  outliers start: 16
  outliers final: 14
  residues processed: 102
  average time/residue: 0.0884
  time to fit residues: 11.6875
Evaluate side-chains
  106 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   65 THR
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  192 THR
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  566 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 56 optimal weight:    0.4980
   chunk 19 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3992 r_free = 0.3992 target = 0.171931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.141890 restraints weight = 6730.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 2.01
r_work: 0.3446 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   6044  Z= 0.194
  Angle     :  0.626  13.558   8219  Z= 0.324
  Chirality :  0.043   0.162    899
  Planarity :  0.004   0.037   1013
  Dihedral  :  4.471  17.315    819
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 13.45 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.12 (0.31), residues: 738
  helix:  1.15 (0.26), residues: 377
  sheet: -0.95 (0.45), residues: 115
  loop : -0.97 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  98 
 TYR   0.019   0.002   TYR A 137 
 PHE   0.019   0.002   PHE A 455 
 TRP   0.016   0.001   TRP A 218 
 HIS   0.004   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 6041)
  covalent geometry    : angle       0.62596 ( 8213)
  SS BOND              : bond        0.00177 (    3)
  SS BOND              : angle       1.08859 (    6)
  hydrogen bonds       : bond        0.04543 (  318)
  hydrogen bonds       : angle       4.86816 (  921)

********************** 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
  110 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.207 
Fit side-chains
REVERT: L  107 MET cc_start: 0.8293 (mmm) cc_final: 0.8056 (mmt)
REVERT: A  212 ASN cc_start: 0.7985 (t0) cc_final: 0.7764 (t0)
REVERT: A  388 SER cc_start: 0.8983 (t) cc_final: 0.8412 (p)
REVERT: A  441 LEU cc_start: 0.8474 (mp) cc_final: 0.8211 (mm)
REVERT: A  498 TYR cc_start: 0.8933 (p90) cc_final: 0.8720 (p90)
REVERT: A  567 ARG cc_start: 0.8237 (mtm-85) cc_final: 0.7803 (mtt180)
  outliers start: 14
  outliers final: 14
  residues processed: 103
  average time/residue: 0.0891
  time to fit residues: 11.8300
Evaluate side-chains
  110 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   65 THR
Chi-restraints excluded: chain H residue   87 ARG
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain L residue   11 MET
Chi-restraints excluded: chain L residue   98 THR
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  566 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 18 optimal weight:    0.3980
   chunk 49 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 33 optimal weight:    0.4980
   chunk 58 optimal weight:    1.9990
   chunk 21 optimal weight:    0.1980
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.4014 r_free = 0.4014 target = 0.173983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.142396 restraints weight = 6630.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 1.91
r_work: 0.3479 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3332 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6044  Z= 0.157
  Angle     :  0.619  13.272   8219  Z= 0.315
  Chirality :  0.042   0.173    899
  Planarity :  0.004   0.038   1013
  Dihedral  :  4.402  16.882    819
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 13.61 %
    Favored  : 84.18 %
  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:  0.20 (0.31), residues: 738
  helix:  1.21 (0.26), residues: 377
  sheet: -0.87 (0.45), residues: 115
  loop : -0.96 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  98 
 TYR   0.021   0.001   TYR A 137 
 PHE   0.016   0.001   PHE A 300 
 TRP   0.015   0.001   TRP A 218 
 HIS   0.004   0.001   HIS H  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 6041)
  covalent geometry    : angle       0.61888 ( 8213)
  SS BOND              : bond        0.00204 (    3)
  SS BOND              : angle       0.88656 (    6)
  hydrogen bonds       : bond        0.04334 (  318)
  hydrogen bonds       : angle       4.79791 (  921)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1751.22 seconds
wall clock time: 30 minutes 47.30 seconds (1847.30 seconds total)