Starting phenix.real_space_refine
on Tue Mar  3 13:07:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qic_13987/03_2026/7qic_13987.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qic_13987/03_2026/7qic_13987.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qic_13987/03_2026/7qic_13987.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qic_13987/03_2026/7qic_13987.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qic_13987/03_2026/7qic_13987.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qic_13987/03_2026/7qic_13987.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.036
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
     Mg      1      5.21       5
     S      28      5.16       5
     C    3148      2.51       5
     N     809      2.21       5
     O     855      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4841
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2991
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 2991
          Classifications: {'peptide': 401}
          Link IDs: {'PTRANS': 12, 'TRANS': 388}
    Chain: "C"
      Number of atoms: 908
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 908
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 5, 'TRANS': 111}
    Chain: "B"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 941
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 4, 'TRANS': 116}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.17, per 1000 atoms: 0.24
  Number of scatterers: 4841
  At special positions: 0
  Unit cell: (88.536, 105.462, 76.818, 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)
     S      28     16.00
     Mg      1     11.99
     O     855      8.00
     N     809      7.00
     C    3148      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " 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: 0.29
  Conformation dependent library (CDL) restraints added in 318.1 milliseconds
  

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1166

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 5 sheets defined
      55.4% alpha, 7.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 43
    Processing helix  chain 'A' and resid 43 through 53
    Processing helix  chain 'A' and resid 57 through 70
      removed outlier: 3.519A  pdb=" N   THR A  61 " --> pdb=" O   GLY A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 74
      removed outlier: 3.666A  pdb=" N   LEU A  74 " --> pdb=" O   PHE A  71 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 71 through 74'
    Processing helix  chain 'A' and resid 75 through 99
      removed outlier: 4.061A  pdb=" N   ILE A  79 " --> pdb=" O   TRP A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 110
    Processing helix  chain 'A' and resid 111 through 144
      removed outlier: 3.955A  pdb=" N   PHE A 144 " --> pdb=" O   GLY A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 165
    Processing helix  chain 'A' and resid 169 through 179
    Processing helix  chain 'A' and resid 180 through 192
      removed outlier: 4.103A  pdb=" N   THR A 184 " --> pdb=" O   LEU A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 202
    Processing helix  chain 'A' and resid 211 through 227
    Processing helix  chain 'A' and resid 228 through 242
      removed outlier: 3.793A  pdb=" N   PHE A 232 " --> pdb=" O   PRO A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 277
      removed outlier: 3.536A  pdb=" N   GLN A 251 " --> pdb=" O   ASP A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 292
      removed outlier: 3.851A  pdb=" N   ARG A 292 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 299
    Processing helix  chain 'A' and resid 301 through 333
      removed outlier: 3.641A  pdb=" N   PHE A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ALA A 307 " --> pdb=" O   GLU A 303 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ALA A 318 " --> pdb=" O   SER A 314 " (cutoff:3.500A)
      Proline residue:  A 322  - end of helix
      removed outlier: 3.631A  pdb=" N   THR A 325 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   PHE A 333 " --> pdb=" O   ILE A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 345
      removed outlier: 4.261A  pdb=" N   GLU A 345 " --> pdb=" O   LYS A 342 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 342 through 345'
    Processing helix  chain 'A' and resid 346 through 364
      removed outlier: 3.570A  pdb=" N   LYS A 350 " --> pdb=" O   ALA A 346 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   VAL A 364 " --> pdb=" O   SER A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 385
      removed outlier: 4.010A  pdb=" N   GLN A 379 " --> pdb=" O   MET A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 399
      removed outlier: 4.013A  pdb=" N   LEU A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 404
      removed outlier: 4.327A  pdb=" N   MET A 403 " --> pdb=" O   ASP A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 437
    Processing helix  chain 'B' and resid 108 through 112
      removed outlier: 3.994A  pdb=" N   GLU B 111 " --> pdb=" O   ASP B 108 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   TYR B 112 " --> pdb=" O   PRO B 109 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 108 through 112'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 5 through 7
      removed outlier: 3.998A  pdb=" N   GLU C  23 " --> pdb=" O   VAL C   5 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   SER C   7 " --> pdb=" O   SER C  21 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   SER C  21 " --> pdb=" O   SER C   7 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   THR C  68 " --> pdb=" O   GLN C  81 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 33 through 35
      removed outlier: 3.816A  pdb=" N   ALA C  33 " --> pdb=" O   ASP C  98 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ASP C  98 " --> pdb=" O   ALA C  33 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 93
    Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 20
      removed outlier: 3.859A  pdb=" N   LEU B  18 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 60
      removed outlier: 3.510A  pdb=" N   ALA B  50 " --> pdb=" O   ASN B  59 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   VAL B  48 " --> pdb=" O   TRP B  36 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   GLY B  35 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ALA B  97 " --> pdb=" O   GLY B  35 " (cutoff:3.500A)

    267 hydrogen bonds defined for protein.
    771 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: 0.60

  Time building geometry restraints manager: 0.44 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1530
        1.34 -     1.46: 1163
        1.46 -     1.58: 2201
        1.58 -     1.70: 0
        1.70 -     1.82: 48
  Bond restraints: 4942
  Sorted by residual:
  bond pdb=" CA  TYR A 168 "
       pdb=" C   TYR A 168 "
    ideal  model  delta    sigma   weight residual
    1.523  1.537 -0.013 1.34e-02 5.57e+03 1.00e+00
  bond pdb=" CA  VAL A 205 "
       pdb=" CB  VAL A 205 "
    ideal  model  delta    sigma   weight residual
    1.526  1.540 -0.014 1.55e-02 4.16e+03 7.93e-01
  bond pdb=" CA  TYR A 168 "
       pdb=" CB  TYR A 168 "
    ideal  model  delta    sigma   weight residual
    1.530  1.544 -0.014 1.69e-02 3.50e+03 7.05e-01
  bond pdb=" CA  CYS C  95 "
       pdb=" CB  CYS C  95 "
    ideal  model  delta    sigma   weight residual
    1.527  1.548 -0.020 2.48e-02 1.63e+03 6.73e-01
  bond pdb=" N   TYR A 168 "
       pdb=" CA  TYR A 168 "
    ideal  model  delta    sigma   weight residual
    1.457  1.468 -0.011 1.29e-02 6.01e+03 6.67e-01
  ... (remaining 4937 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 6534
        1.66 -     3.32: 148
        3.32 -     4.98: 28
        4.98 -     6.64: 9
        6.64 -     8.30: 2
  Bond angle restraints: 6721
  Sorted by residual:
  angle pdb=" N   GLU B  89 "
        pdb=" CA  GLU B  89 "
        pdb=" CB  GLU B  89 "
      ideal   model   delta    sigma   weight residual
     112.78  108.06    4.72 1.53e+00 4.27e-01 9.53e+00
  angle pdb=" CA  ASN C  83 "
        pdb=" C   ASN C  83 "
        pdb=" O   ASN C  83 "
      ideal   model   delta    sigma   weight residual
     121.67  118.16    3.51 1.26e+00 6.30e-01 7.74e+00
  angle pdb=" N   ASN C  32 "
        pdb=" CA  ASN C  32 "
        pdb=" C   ASN C  32 "
      ideal   model   delta    sigma   weight residual
     113.43  110.05    3.38 1.26e+00 6.30e-01 7.21e+00
  angle pdb=" C   THR A 130 "
        pdb=" N   PHE A 131 "
        pdb=" CA  PHE A 131 "
      ideal   model   delta    sigma   weight residual
     120.72  116.25    4.47 1.67e+00 3.59e-01 7.18e+00
  angle pdb=" CB  MET A  89 "
        pdb=" CG  MET A  89 "
        pdb=" SD  MET A  89 "
      ideal   model   delta    sigma   weight residual
     112.70  104.93    7.77 3.00e+00 1.11e-01 6.71e+00
  ... (remaining 6716 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.91: 2615
       15.91 -    31.82: 202
       31.82 -    47.73: 61
       47.73 -    63.64: 8
       63.64 -    79.55: 3
  Dihedral angle restraints: 2889
    sinusoidal: 1068
      harmonic: 1821
  Sorted by residual:
  dihedral pdb=" CA  GLN B 117 "
           pdb=" C   GLN B 117 "
           pdb=" N   GLY B 118 "
           pdb=" CA  GLY B 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.53   19.47     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  96 "
           pdb=" CB  CYS B  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  124.62  -31.62     1      1.00e+01 1.00e-02 1.43e+01
  dihedral pdb=" CA  VAL C  28 "
           pdb=" C   VAL C  28 "
           pdb=" N   PHE C  29 "
           pdb=" CA  PHE C  29 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.49   18.51     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 2886 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 476
       0.036 -    0.071: 238
       0.071 -    0.106: 66
       0.106 -    0.142: 13
       0.142 -    0.177: 2
  Chirality restraints: 795
  Sorted by residual:
  chirality pdb=" CA  PHE A 131 "
            pdb=" N   PHE A 131 "
            pdb=" C   PHE A 131 "
            pdb=" CB  PHE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.88e-01
  chirality pdb=" CB  THR C  90 "
            pdb=" CA  THR C  90 "
            pdb=" OG1 THR C  90 "
            pdb=" CG2 THR C  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.15 2.00e-01 2.50e+01 5.36e-01
  chirality pdb=" CA  PRO A 228 "
            pdb=" N   PRO A 228 "
            pdb=" C   PRO A 228 "
            pdb=" CB  PRO A 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.30e-01
  ... (remaining 792 not shown)

  Planarity restraints: 837
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C  13 "    0.044 5.00e-02 4.00e+02   6.71e-02 7.20e+00
        pdb=" N   PRO C  14 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO C  14 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO C  14 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 309 "   -0.009 2.00e-02 2.50e+03   1.73e-02 2.99e+00
        pdb=" C   GLY A 309 "    0.030 2.00e-02 2.50e+03
        pdb=" O   GLY A 309 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU A 310 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 131 "    0.014 2.00e-02 2.50e+03   1.30e-02 2.98e+00
        pdb=" CG  PHE A 131 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 131 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 131 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 131 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 131 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 131 "    0.001 2.00e-02 2.50e+03
  ... (remaining 834 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 694
        2.76 -     3.29: 4843
        3.29 -     3.83: 7905
        3.83 -     4.36: 8604
        4.36 -     4.90: 15115
  Nonbonded interactions: 37161
  Sorted by model distance:
  nonbonded pdb=" O   TYR B  94 "
            pdb=" OG1 THR B 119 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OH  TYR C  37 "
            pdb=" O   LEU C 103 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   ASN A 126 "
            pdb=" OG1 THR A 130 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   ARG B  52 "
            pdb=" NH1 ARG B  72 "
     model   vdw
     2.306 3.120
  nonbonded pdb=" OG1 THR A 129 "
            pdb=" ND2 ASN A 382 "
     model   vdw
     2.341 3.120
  ... (remaining 37156 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.390
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.920
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
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      :  0.003   0.034   4944  Z= 0.135
  Angle     :  0.650   8.303   6725  Z= 0.350
  Chirality :  0.043   0.177    795
  Planarity :  0.005   0.067    837
  Dihedral  : 12.831  79.553   1717
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.40 %
    Favored  : 99.40 %
  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 are not related in a simple way.
  whole: -0.78 (0.34), residues: 633
  helix:  0.77 (0.30), residues: 305
  sheet: -1.57 (0.63), residues: 73
  loop : -1.78 (0.38), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  19 
 TYR   0.009   0.001   TYR A 185 
 PHE   0.030   0.001   PHE A 131 
 TRP   0.008   0.001   TRP A 160 
 HIS   0.001   0.000   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4942)
  covalent geometry    : angle       0.65041 ( 6721)
  SS BOND              : bond        0.00124 (    2)
  SS BOND              : angle       0.58431 (    4)
  hydrogen bonds       : bond        0.17168 (  267)
  hydrogen bonds       : angle       6.88654 (  771)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A  120 LEU cc_start: 0.7446 (tt) cc_final: 0.7146 (mm)
REVERT: A  182 PHE cc_start: 0.6387 (m-10) cc_final: 0.6105 (m-10)
REVERT: A  246 LYS cc_start: 0.8682 (tttm) cc_final: 0.8178 (tptt)
REVERT: C   14 PRO cc_start: 0.8515 (Cg_endo) cc_final: 0.8214 (Cg_exo)
  outliers start: 1
  outliers final: 0
  residues processed: 145
  average time/residue: 0.0640
  time to fit residues: 12.0995
Evaluate side-chains
  119 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 61 optimal weight:    0.3980
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  32 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.159298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.130772 restraints weight = 7226.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.130876 restraints weight = 6610.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.131134 restraints weight = 6774.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.131736 restraints weight = 5827.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.131978 restraints weight = 5428.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4944  Z= 0.148
  Angle     :  0.599   5.926   6725  Z= 0.318
  Chirality :  0.043   0.184    795
  Planarity :  0.005   0.052    837
  Dihedral  :  4.298  21.535    686
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.37 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  5.98 %
    Favored  : 93.63 %
  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 are not related in a simple way.
  whole: -0.36 (0.34), residues: 633
  helix:  1.23 (0.29), residues: 314
  sheet: -1.38 (0.65), residues: 73
  loop : -1.84 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  19 
 TYR   0.014   0.001   TYR A 185 
 PHE   0.033   0.002   PHE A 131 
 TRP   0.011   0.001   TRP A 229 
 HIS   0.001   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 4942)
  covalent geometry    : angle       0.59917 ( 6721)
  SS BOND              : bond        0.00108 (    2)
  SS BOND              : angle       0.56836 (    4)
  hydrogen bonds       : bond        0.04400 (  267)
  hydrogen bonds       : angle       5.13168 (  771)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 141
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A   80 MET cc_start: 0.8644 (mmp) cc_final: 0.8305 (mmt)
REVERT: A  191 MET cc_start: 0.7158 (ttp) cc_final: 0.6955 (ttp)
REVERT: A  246 LYS cc_start: 0.8791 (tttm) cc_final: 0.8270 (tptt)
REVERT: A  319 CYS cc_start: 0.8115 (m) cc_final: 0.7706 (t)
REVERT: B   47 PHE cc_start: 0.8663 (t80) cc_final: 0.8351 (t80)
  outliers start: 2
  outliers final: 0
  residues processed: 142
  average time/residue: 0.0687
  time to fit residues: 12.5858
Evaluate side-chains
  117 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 58 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 47 optimal weight:    4.9990
   chunk 52 optimal weight:    8.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
C  32 ASN
C  58 ASN
C  73 ASN
C  76 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.153036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.133832 restraints weight = 6599.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.133321 restraints weight = 7018.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.133819 restraints weight = 6882.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.134246 restraints weight = 5971.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.134354 restraints weight = 5483.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4944  Z= 0.152
  Angle     :  0.607   6.628   6725  Z= 0.321
  Chirality :  0.043   0.195    795
  Planarity :  0.004   0.054    837
  Dihedral  :  4.358  22.246    686
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.21 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  3.59 %
    Favored  : 96.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.34), residues: 633
  helix:  1.26 (0.29), residues: 315
  sheet: -1.39 (0.64), residues: 73
  loop : -1.94 (0.38), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  86 
 TYR   0.011   0.001   TYR A 185 
 PHE   0.019   0.002   PHE C  50 
 TRP   0.010   0.001   TRP B  53 
 HIS   0.001   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 4942)
  covalent geometry    : angle       0.60741 ( 6721)
  SS BOND              : bond        0.00188 (    2)
  SS BOND              : angle       0.56912 (    4)
  hydrogen bonds       : bond        0.04205 (  267)
  hydrogen bonds       : angle       4.82279 (  771)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 MET cc_start: 0.8827 (mmp) cc_final: 0.8338 (mmt)
REVERT: A  246 LYS cc_start: 0.8590 (tttm) cc_final: 0.8205 (tptt)
REVERT: A  252 LYS cc_start: 0.7966 (tptm) cc_final: 0.7483 (ttpt)
REVERT: A  319 CYS cc_start: 0.8279 (m) cc_final: 0.7879 (t)
REVERT: C   14 PRO cc_start: 0.8621 (Cg_exo) cc_final: 0.8390 (Cg_endo)
REVERT: B   47 PHE cc_start: 0.8569 (t80) cc_final: 0.8354 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0601
  time to fit residues: 10.8854
Evaluate side-chains
  120 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 53 optimal weight:    0.2980
   chunk 30 optimal weight:    8.9990
   chunk 18 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
C  13 GLN
C  32 ASN
C  73 ASN
C  76 ASN
B  31 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.148613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.126918 restraints weight = 6627.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.128321 restraints weight = 5230.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.129029 restraints weight = 4453.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.130051 restraints weight = 4053.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.130051 restraints weight = 3733.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   4944  Z= 0.190
  Angle     :  0.654   6.294   6725  Z= 0.339
  Chirality :  0.044   0.194    795
  Planarity :  0.005   0.056    837
  Dihedral  :  4.422  22.852    686
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.69 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  4.58 %
    Favored  : 95.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.34), residues: 633
  helix:  1.20 (0.29), residues: 315
  sheet: -1.35 (0.65), residues: 73
  loop : -2.04 (0.38), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  86 
 TYR   0.014   0.002   TYR A 185 
 PHE   0.023   0.002   PHE C  50 
 TRP   0.017   0.001   TRP B  53 
 HIS   0.001   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 4942)
  covalent geometry    : angle       0.65348 ( 6721)
  SS BOND              : bond        0.00268 (    2)
  SS BOND              : angle       0.74331 (    4)
  hydrogen bonds       : bond        0.04272 (  267)
  hydrogen bonds       : angle       4.78695 (  771)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: A  142 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7613 (tm-30)
REVERT: A  246 LYS cc_start: 0.8580 (tttm) cc_final: 0.8174 (tptt)
REVERT: A  319 CYS cc_start: 0.8294 (m) cc_final: 0.7923 (t)
REVERT: C   14 PRO cc_start: 0.8793 (Cg_exo) cc_final: 0.8125 (Cg_endo)
REVERT: B   47 PHE cc_start: 0.8580 (t80) cc_final: 0.8226 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0611
  time to fit residues: 11.1459
Evaluate side-chains
  113 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0020
   chunk 15 optimal weight:    0.3980
   chunk 40 optimal weight:    0.0770
   chunk 14 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 38 optimal weight:    0.3980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.2946

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 ASN
C  13 GLN
C  32 ASN
C  73 ASN
C  76 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.160737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.135097 restraints weight = 7089.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.133693 restraints weight = 6792.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.135234 restraints weight = 7195.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.135485 restraints weight = 5810.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.135860 restraints weight = 5090.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4944  Z= 0.125
  Angle     :  0.596   7.093   6725  Z= 0.311
  Chirality :  0.043   0.175    795
  Planarity :  0.004   0.056    837
  Dihedral  :  4.369  21.816    686
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.27 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.99 %
    Favored  : 96.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.34), residues: 633
  helix:  1.39 (0.30), residues: 311
  sheet: -1.53 (0.59), residues: 84
  loop : -1.88 (0.39), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  86 
 TYR   0.011   0.001   TYR A 185 
 PHE   0.022   0.002   PHE C  50 
 TRP   0.009   0.001   TRP B  53 
 HIS   0.001   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 4942)
  covalent geometry    : angle       0.59623 ( 6721)
  SS BOND              : bond        0.00170 (    2)
  SS BOND              : angle       0.34244 (    4)
  hydrogen bonds       : bond        0.03746 (  267)
  hydrogen bonds       : angle       4.63540 (  771)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A   89 MET cc_start: 0.7676 (tpt) cc_final: 0.7457 (ttp)
REVERT: A  107 ARG cc_start: 0.7613 (tpp80) cc_final: 0.7043 (ttt180)
REVERT: A  246 LYS cc_start: 0.8742 (tttm) cc_final: 0.8266 (tptt)
REVERT: C   14 PRO cc_start: 0.8844 (Cg_exo) cc_final: 0.8275 (Cg_endo)
REVERT: C   58 ASN cc_start: 0.8770 (p0) cc_final: 0.8175 (p0)
REVERT: B   47 PHE cc_start: 0.8643 (t80) cc_final: 0.8336 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0560
  time to fit residues: 10.4352
Evaluate side-chains
  118 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0470
   chunk 47 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.7480

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  13 GLN
C  32 ASN
C  73 ASN
C  76 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.160841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.134681 restraints weight = 7232.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.134017 restraints weight = 6080.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.134448 restraints weight = 5909.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.134759 restraints weight = 5465.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.134939 restraints weight = 5196.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4944  Z= 0.149
  Angle     :  0.620   6.170   6725  Z= 0.321
  Chirality :  0.043   0.184    795
  Planarity :  0.005   0.073    837
  Dihedral  :  4.351  22.323    686
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.39 %
    Favored  : 98.41 %
  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 are not related in a simple way.
  whole: -0.28 (0.34), residues: 633
  helix:  1.38 (0.29), residues: 310
  sheet: -1.47 (0.61), residues: 84
  loop : -1.83 (0.39), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  86 
 TYR   0.015   0.001   TYR A 185 
 PHE   0.025   0.002   PHE A 327 
 TRP   0.014   0.001   TRP B  53 
 HIS   0.001   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 4942)
  covalent geometry    : angle       0.61984 ( 6721)
  SS BOND              : bond        0.00126 (    2)
  SS BOND              : angle       0.44434 (    4)
  hydrogen bonds       : bond        0.03959 (  267)
  hydrogen bonds       : angle       4.59740 (  771)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A  246 LYS cc_start: 0.8766 (tttm) cc_final: 0.8284 (tptt)
REVERT: C   14 PRO cc_start: 0.8841 (Cg_exo) cc_final: 0.8260 (Cg_endo)
REVERT: C   58 ASN cc_start: 0.8842 (p0) cc_final: 0.8340 (p0)
REVERT: B   47 PHE cc_start: 0.8575 (t80) cc_final: 0.8259 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0528
  time to fit residues: 9.9453
Evaluate side-chains
  111 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 36 optimal weight:    8.9990
   chunk 56 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 33 optimal weight:    0.3980
   chunk 26 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
C  13 GLN
C  32 ASN
C  73 ASN
C  76 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.158477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.130773 restraints weight = 7102.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.130331 restraints weight = 6021.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.131281 restraints weight = 5835.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.131721 restraints weight = 5194.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.132106 restraints weight = 4742.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4944  Z= 0.147
  Angle     :  0.619   6.889   6725  Z= 0.321
  Chirality :  0.044   0.199    795
  Planarity :  0.005   0.060    837
  Dihedral  :  4.338  21.818    686
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.59 %
    Favored  : 97.21 %
  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 are not related in a simple way.
  whole: -0.30 (0.34), residues: 633
  helix:  1.36 (0.29), residues: 312
  sheet: -1.46 (0.61), residues: 84
  loop : -1.86 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C  86 
 TYR   0.012   0.001   TYR A 185 
 PHE   0.027   0.002   PHE C  50 
 TRP   0.015   0.001   TRP B  53 
 HIS   0.001   0.000   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 4942)
  covalent geometry    : angle       0.61870 ( 6721)
  SS BOND              : bond        0.00230 (    2)
  SS BOND              : angle       0.40554 (    4)
  hydrogen bonds       : bond        0.03895 (  267)
  hydrogen bonds       : angle       4.54285 (  771)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: A  246 LYS cc_start: 0.8829 (tttm) cc_final: 0.8254 (tptt)
REVERT: C   14 PRO cc_start: 0.8817 (Cg_exo) cc_final: 0.8280 (Cg_endo)
REVERT: C   58 ASN cc_start: 0.8821 (p0) cc_final: 0.8431 (p0)
REVERT: B   47 PHE cc_start: 0.8559 (t80) cc_final: 0.8246 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0509
  time to fit residues: 9.7592
Evaluate side-chains
  110 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 33 optimal weight:    0.2980
   chunk 47 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0980
   chunk 16 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
C  13 GLN
C  32 ASN
C  73 ASN
C  76 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.160422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.132969 restraints weight = 7231.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.132749 restraints weight = 6196.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.133621 restraints weight = 5997.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.134034 restraints weight = 5306.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.134311 restraints weight = 4806.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4944  Z= 0.133
  Angle     :  0.622   6.935   6725  Z= 0.323
  Chirality :  0.044   0.184    795
  Planarity :  0.005   0.054    837
  Dihedral  :  4.332  21.766    686
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.60 %
    Favored  : 99.20 %
  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 are not related in a simple way.
  whole: -0.23 (0.34), residues: 633
  helix:  1.46 (0.29), residues: 311
  sheet: -1.53 (0.61), residues: 84
  loop : -1.83 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  86 
 TYR   0.012   0.001   TYR A 185 
 PHE   0.026   0.001   PHE C  50 
 TRP   0.012   0.001   TRP B  53 
 HIS   0.001   0.000   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4942)
  covalent geometry    : angle       0.62229 ( 6721)
  SS BOND              : bond        0.00122 (    2)
  SS BOND              : angle       0.34055 (    4)
  hydrogen bonds       : bond        0.03767 (  267)
  hydrogen bonds       : angle       4.48818 (  771)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A   89 MET cc_start: 0.7756 (tpt) cc_final: 0.7407 (ttp)
REVERT: A  246 LYS cc_start: 0.8764 (tttm) cc_final: 0.8294 (tptt)
REVERT: C   14 PRO cc_start: 0.8843 (Cg_exo) cc_final: 0.8416 (Cg_endo)
REVERT: C   58 ASN cc_start: 0.8789 (p0) cc_final: 0.8332 (p0)
REVERT: B   47 PHE cc_start: 0.8559 (t80) cc_final: 0.8248 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 139
  average time/residue: 0.0515
  time to fit residues: 9.8575
Evaluate side-chains
  114 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 51 optimal weight:    9.9990
   chunk 47 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0870
   chunk 4 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  13 GLN
C  32 ASN
C  76 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.160901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.134576 restraints weight = 7119.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.134275 restraints weight = 6165.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.135054 restraints weight = 6160.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.135399 restraints weight = 5485.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.135708 restraints weight = 4993.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4944  Z= 0.135
  Angle     :  0.616   7.646   6725  Z= 0.318
  Chirality :  0.044   0.183    795
  Planarity :  0.005   0.064    837
  Dihedral  :  4.314  21.461    686
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  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 are not related in a simple way.
  whole: -0.17 (0.34), residues: 633
  helix:  1.51 (0.29), residues: 311
  sheet: -1.48 (0.61), residues: 84
  loop : -1.82 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  86 
 TYR   0.012   0.001   TYR A 185 
 PHE   0.021   0.002   PHE C  50 
 TRP   0.011   0.001   TRP B  53 
 HIS   0.001   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4942)
  covalent geometry    : angle       0.61607 ( 6721)
  SS BOND              : bond        0.00206 (    2)
  SS BOND              : angle       0.37893 (    4)
  hydrogen bonds       : bond        0.03757 (  267)
  hydrogen bonds       : angle       4.47745 (  771)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A  246 LYS cc_start: 0.8728 (tttm) cc_final: 0.8257 (tptt)
REVERT: C   14 PRO cc_start: 0.8859 (Cg_exo) cc_final: 0.8423 (Cg_endo)
REVERT: C   58 ASN cc_start: 0.8789 (p0) cc_final: 0.8149 (p0)
REVERT: B   47 PHE cc_start: 0.8535 (t80) cc_final: 0.8224 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.0538
  time to fit residues: 9.9538
Evaluate side-chains
  113 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 51 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0270
   chunk 50 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
C  13 GLN
C  32 ASN
C  76 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.160131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.130373 restraints weight = 7177.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.132482 restraints weight = 6477.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.133109 restraints weight = 5087.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.133939 restraints weight = 4682.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.134053 restraints weight = 4322.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4944  Z= 0.136
  Angle     :  0.620   8.586   6725  Z= 0.323
  Chirality :  0.044   0.182    795
  Planarity :  0.005   0.062    837
  Dihedral  :  4.296  21.485    686
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.60 %
    Favored  : 99.20 %
  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 are not related in a simple way.
  whole: -0.15 (0.35), residues: 633
  helix:  1.57 (0.29), residues: 311
  sheet: -1.66 (0.58), residues: 90
  loop : -1.79 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  86 
 TYR   0.012   0.001   TYR A 185 
 PHE   0.020   0.001   PHE C  50 
 TRP   0.013   0.001   TRP B  53 
 HIS   0.001   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 4942)
  covalent geometry    : angle       0.61973 ( 6721)
  SS BOND              : bond        0.00160 (    2)
  SS BOND              : angle       0.34553 (    4)
  hydrogen bonds       : bond        0.03778 (  267)
  hydrogen bonds       : angle       4.48052 (  771)

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

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

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1266 Ramachandran restraints generated.
    633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 133
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 LEU cc_start: 0.7582 (tt) cc_final: 0.7221 (mm)
REVERT: A  246 LYS cc_start: 0.8805 (tttm) cc_final: 0.8244 (tptt)
REVERT: A  372 MET cc_start: 0.8966 (mmm) cc_final: 0.8573 (tpt)
REVERT: C   14 PRO cc_start: 0.8835 (Cg_exo) cc_final: 0.8447 (Cg_endo)
REVERT: C   58 ASN cc_start: 0.8789 (p0) cc_final: 0.8231 (p0)
REVERT: B   47 PHE cc_start: 0.8583 (t80) cc_final: 0.8274 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 134
  average time/residue: 0.0542
  time to fit residues: 9.9589
Evaluate side-chains
  111 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 59 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  13 GLN
C  32 ASN
C  76 ASN
** B  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.158286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.132604 restraints weight = 7218.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.131444 restraints weight = 6963.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.132219 restraints weight = 7689.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.132932 restraints weight = 5976.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.133406 restraints weight = 5457.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4944  Z= 0.161
  Angle     :  0.648   7.608   6725  Z= 0.338
  Chirality :  0.044   0.179    795
  Planarity :  0.005   0.051    837
  Dihedral  :  4.356  22.345    686
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.69 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  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 are not related in a simple way.
  whole: -0.19 (0.34), residues: 633
  helix:  1.48 (0.29), residues: 312
  sheet: -1.55 (0.58), residues: 90
  loop : -1.78 (0.41), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 109 
 TYR   0.022   0.001   TYR A 185 
 PHE   0.020   0.002   PHE C  50 
 TRP   0.013   0.001   TRP B  53 
 HIS   0.001   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 4942)
  covalent geometry    : angle       0.64781 ( 6721)
  SS BOND              : bond        0.00191 (    2)
  SS BOND              : angle       0.39247 (    4)
  hydrogen bonds       : bond        0.04009 (  267)
  hydrogen bonds       : angle       4.54680 (  771)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 841.03 seconds
wall clock time: 15 minutes 10.20 seconds (910.20 seconds total)