Starting phenix.real_space_refine
on Thu Jul  2 07:25:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uo2_64370/07_2026/9uo2_64370.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uo2_64370/07_2026/9uo2_64370.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uo2_64370/07_2026/9uo2_64370.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uo2_64370/07_2026/9uo2_64370.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uo2_64370/07_2026/9uo2_64370.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uo2_64370/07_2026/9uo2_64370.map"
  }
  resolution = 2.6
  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=   0.058
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
     P       8      5.49       5
     S      52      5.16       5
     C    5186      2.51       5
     N     958      2.21       5
     O    1118      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7322
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2525
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2525
          Classifications: {'peptide': 327}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 307}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "B"
      Number of atoms: 364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 364
          Classifications: {'peptide': 46}
          Link IDs: {'PTRANS': 1, 'TRANS': 44}
    Chain: "C"
      Number of atoms: 2525
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2525
          Classifications: {'peptide': 327}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 307}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "D"
      Number of atoms: 364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 364
          Classifications: {'peptide': 46}
          Link IDs: {'PTRANS': 1, 'TRANS': 44}
    Chain: "A"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 716
          Unusual residues: {'76F': 2, 'CLR': 17, 'LPE': 1, 'NAG': 1, 'P0E': 1, 'PLM': 7}
          Classifications: {'undetermined': 29}
          Link IDs: {None: 28}
          Unresolved non-hydrogen bonds: 86
          Unresolved non-hydrogen angles: 94
          Unresolved non-hydrogen dihedrals: 88
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'76F:plan-3': 1, 'PLM:plan-1': 7}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'CLR': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 716
          Unusual residues: {'76F': 2, 'CLR': 17, 'LPE': 1, 'NAG': 1, 'P0E': 1, 'PLM': 7}
          Classifications: {'undetermined': 29}
          Link IDs: {None: 28}
          Unresolved non-hydrogen bonds: 86
          Unresolved non-hydrogen angles: 94
          Unresolved non-hydrogen dihedrals: 88
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'76F:plan-3': 1, 'PLM:plan-1': 7}
          Unresolved non-hydrogen planarities: 9
    Chain: "D"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'CLR': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.59, per 1000 atoms: 0.22
  Number of scatterers: 7322
  At special positions: 0
  Unit cell: (81.576, 70.04, 98.88, 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      52     16.00
     P       8     15.00
     O    1118      8.00
     N     958      7.00
     C    5186      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  32 " - pdb=" SG  CYS A 284 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  32 " - pdb=" SG  CYS C 284 " 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=4, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 418 " - " ASN A  25 "
      " NAG C 420 " - " ASN C  25 "
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 321.6 milliseconds
  

  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:  1408

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 2 sheets defined
      79.4% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 25
    Processing helix  chain 'A' and resid 29 through 33
    Processing helix  chain 'A' and resid 38 through 46
    Processing helix  chain 'A' and resid 47 through 79
    Processing helix  chain 'A' and resid 81 through 93
    Processing helix  chain 'A' and resid 93 through 108
    Processing helix  chain 'A' and resid 111 through 139
      removed outlier: 3.866A  pdb=" N   TYR A 128 " --> pdb=" O   ALA A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 148
    Processing helix  chain 'A' and resid 160 through 164
      removed outlier: 3.996A  pdb=" N   CYS A 163 " --> pdb=" O   CYS A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 202
      Proline residue:  A 184  - end of helix
    Processing helix  chain 'A' and resid 216 through 247
      removed outlier: 4.043A  pdb=" N   TRP A 220 " --> pdb=" O   SER A 216 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   GLN A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 250
      No H-bonds generated for 'chain 'A' and resid 248 through 250'
    Processing helix  chain 'A' and resid 251 through 280
      removed outlier: 4.037A  pdb=" N   GLN A 269 " --> pdb=" O   LEU A 265 " (cutoff:3.500A)
      Proline residue:  A 270  - end of helix
    Processing helix  chain 'A' and resid 289 through 318
    Processing helix  chain 'B' and resid 18 through 28
    Processing helix  chain 'B' and resid 33 through 62
    Processing helix  chain 'C' and resid 15 through 25
    Processing helix  chain 'C' and resid 29 through 33
    Processing helix  chain 'C' and resid 38 through 46
    Processing helix  chain 'C' and resid 47 through 79
    Processing helix  chain 'C' and resid 81 through 93
    Processing helix  chain 'C' and resid 93 through 108
    Processing helix  chain 'C' and resid 111 through 139
      removed outlier: 3.860A  pdb=" N   TYR C 128 " --> pdb=" O   ALA C 124 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 148
    Processing helix  chain 'C' and resid 160 through 164
      removed outlier: 3.995A  pdb=" N   CYS C 163 " --> pdb=" O   CYS C 160 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 202
      Proline residue:  C 184  - end of helix
    Processing helix  chain 'C' and resid 216 through 247
      removed outlier: 4.014A  pdb=" N   TRP C 220 " --> pdb=" O   SER C 216 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   GLN C 242 " --> pdb=" O   ILE C 238 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 248 through 250
      No H-bonds generated for 'chain 'C' and resid 248 through 250'
    Processing helix  chain 'C' and resid 251 through 280
      removed outlier: 4.029A  pdb=" N   GLN C 269 " --> pdb=" O   LEU C 265 " (cutoff:3.500A)
      Proline residue:  C 270  - end of helix
    Processing helix  chain 'C' and resid 289 through 318
    Processing helix  chain 'D' and resid 18 through 28
    Processing helix  chain 'D' and resid 33 through 62
    Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153
    Processing sheet with id=AA2, first strand: chain 'C' and resid 152 through 153

    452 hydrogen bonds defined for protein.
    1332 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: 1.08

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 901
        1.27 -     1.41: 1466
        1.41 -     1.54: 4788
        1.54 -     1.68: 307
        1.68 -     1.81: 80
  Bond restraints: 7542
  Sorted by residual:
  bond pdb=" N   76F C 403 "
       pdb=" C5  76F C 403 "
    ideal  model  delta    sigma   weight residual
    1.454  1.135  0.319 2.00e-02 2.50e+03 2.55e+02
  bond pdb=" N   76F A 401 "
       pdb=" C5  76F A 401 "
    ideal  model  delta    sigma   weight residual
    1.454  1.136  0.318 2.00e-02 2.50e+03 2.53e+02
  bond pdb=" C21 76F C 403 "
       pdb=" C22 76F C 403 "
    ideal  model  delta    sigma   weight residual
    1.330  1.547 -0.217 2.00e-02 2.50e+03 1.18e+02
  bond pdb=" C21 76F A 401 "
       pdb=" C22 76F A 401 "
    ideal  model  delta    sigma   weight residual
    1.330  1.547 -0.217 2.00e-02 2.50e+03 1.18e+02
  bond pdb=" C40 76F A 401 "
       pdb=" C41 76F A 401 "
    ideal  model  delta    sigma   weight residual
    1.330  1.544 -0.214 2.00e-02 2.50e+03 1.15e+02
  ... (remaining 7537 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    13.53: 10346
       13.53 -    27.05: 14
       27.05 -    40.58: 0
       40.58 -    54.11: 0
       54.11 -    67.63: 2
  Bond angle restraints: 10362
  Sorted by residual:
  angle pdb=" N   76F C 403 "
        pdb=" C5  76F C 403 "
        pdb=" C4  76F C 403 "
      ideal   model   delta    sigma   weight residual
     112.35  179.98  -67.63 3.00e+00 1.11e-01 5.08e+02
  angle pdb=" N   76F A 401 "
        pdb=" C5  76F A 401 "
        pdb=" C4  76F A 401 "
      ideal   model   delta    sigma   weight residual
     112.35  179.13  -66.78 3.00e+00 1.11e-01 4.96e+02
  angle pdb=" CA  VAL C 155 "
        pdb=" C   VAL C 155 "
        pdb=" N   HIS C 156 "
      ideal   model   delta    sigma   weight residual
     118.55  124.88   -6.33 8.60e-01 1.35e+00 5.42e+01
  angle pdb=" O31 LPE A 404 "
        pdb=" P   LPE A 404 "
        pdb=" O32 LPE A 404 "
      ideal   model   delta    sigma   weight residual
     122.76  101.45   21.31 3.00e+00 1.11e-01 5.05e+01
  angle pdb=" O31 LPE C 406 "
        pdb=" P   LPE C 406 "
        pdb=" O32 LPE C 406 "
      ideal   model   delta    sigma   weight residual
     122.76  101.45   21.31 3.00e+00 1.11e-01 5.04e+01
  ... (remaining 10357 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.99: 6158
       31.99 -    63.98: 244
       63.98 -    95.96: 26
       95.96 -   127.95: 14
      127.95 -   159.94: 8
  Dihedral angle restraints: 6450
    sinusoidal: 4276
      harmonic: 2174
  Sorted by residual:
  dihedral pdb=" CA  GLY C 158 "
           pdb=" C   GLY C 158 "
           pdb=" N   PRO C 159 "
           pdb=" CA  PRO C 159 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   73.96  106.04     0      5.00e+00 4.00e-02 4.50e+02
  dihedral pdb=" CA  GLY A 158 "
           pdb=" C   GLY A 158 "
           pdb=" N   PRO A 159 "
           pdb=" CA  PRO A 159 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   73.96  106.04     0      5.00e+00 4.00e-02 4.50e+02
  dihedral pdb=" C19 76F C 404 "
           pdb=" C20 76F C 404 "
           pdb=" C21 76F C 404 "
           pdb=" C22 76F C 404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     113.32  -86.74 -159.94     1      3.00e+01 1.11e-03 2.07e+01
  ... (remaining 6447 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.169: 1291
       0.169 -    0.337: 9
       0.337 -    0.506: 2
       0.506 -    0.674: 0
       0.674 -    0.843: 2
  Chirality restraints: 1304
  Sorted by residual:
  chirality pdb=" C1  NAG A 418 "
            pdb=" ND2 ASN A  25 "
            pdb=" C2  NAG A 418 "
            pdb=" O5  NAG A 418 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.56   -0.84 2.00e-01 2.50e+01 1.78e+01
  chirality pdb=" C1  NAG C 420 "
            pdb=" ND2 ASN C  25 "
            pdb=" C2  NAG C 420 "
            pdb=" O5  NAG C 420 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.61   -0.79 2.00e-01 2.50e+01 1.56e+01
  chirality pdb=" C2  76F C 404 "
            pdb=" C1  76F C 404 "
            pdb=" C3  76F C 404 "
            pdb=" O2  76F C 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.77    0.41 2.00e-01 2.50e+01 4.11e+00
  ... (remaining 1301 not shown)

  Planarity restraints: 1008
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C20 76F A 402 "    0.095 2.00e-02 2.50e+03   1.84e-01 3.40e+02
        pdb=" C21 76F A 402 "   -0.249 2.00e-02 2.50e+03
        pdb=" C22 76F A 402 "    0.240 2.00e-02 2.50e+03
        pdb=" C23 76F A 402 "   -0.086 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C20 76F C 404 "   -0.095 2.00e-02 2.50e+03   1.84e-01 3.40e+02
        pdb=" C21 76F C 404 "    0.249 2.00e-02 2.50e+03
        pdb=" C22 76F C 404 "   -0.240 2.00e-02 2.50e+03
        pdb=" C23 76F C 404 "    0.086 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C17 76F A 402 "    0.162 2.00e-02 2.50e+03   1.59e-01 2.54e+02
        pdb=" C18 76F A 402 "   -0.169 2.00e-02 2.50e+03
        pdb=" C19 76F A 402 "   -0.149 2.00e-02 2.50e+03
        pdb=" C20 76F A 402 "    0.157 2.00e-02 2.50e+03
  ... (remaining 1005 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1577
        2.81 -     3.33: 7053
        3.33 -     3.85: 11592
        3.85 -     4.38: 14365
        4.38 -     4.90: 23881
  Nonbonded interactions: 58468
  Sorted by model distance:
  nonbonded pdb=" SG  CYS A 161 "
            pdb=" C1  PLM A 423 "
     model   vdw
     2.287 3.630
  nonbonded pdb=" SG  CYS C 161 "
            pdb=" C1  PLM C 425 "
     model   vdw
     2.288 3.630
  nonbonded pdb=" NZ  LYS C 141 "
            pdb=" OE1 GLN C 178 "
     model   vdw
     2.289 3.120
  nonbonded pdb=" SG  CYS C 161 "
            pdb=" O2  PLM C 425 "
     model   vdw
     2.291 3.400
  nonbonded pdb=" SG  CYS A 161 "
            pdb=" O2  PLM A 423 "
     model   vdw
     2.292 3.400
  ... (remaining 58463 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: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 2 through 328 or resid 407 through 417 or resid 421 throug \ 
h 422 or (resid 423 through 424 and (name C1 or name C2 or name C3 or name C4 or \ 
 name O2 )) or resid 425 or resid 428 through 429))
  selection = (chain 'C' and (resid 2 through 328 or resid 407 through 417 or (resid 421 and ( \ 
name C1 or name C2 or name C3 or name C4 or name O2 )) or (resid 422 and (name C \ 
1 or name C2 or name C3 or name C4 or name C5 or name C6 or name O2 )) or (resid \ 
 423 through 424 and (name C1 or name C2 or name C3 or name C4 or name O2 )) or  \ 
(resid 425 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 o \ 
r name C7 or name O2 )) or resid 428 through 429))
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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:             2.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.750
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8746
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      :  0.016   0.667   7550  Z= 1.304
  Angle     :  1.475  67.631  10372  Z= 0.575
  Chirality :  0.055   0.843   1304
  Planarity :  0.015   0.184   1006
  Dihedral  : 16.443 159.937   5036
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 15.47 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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:  3.30 (0.31), residues: 738
  helix:  2.90 (0.21), residues: 552
  sheet:  None (None), residues: 0
  loop : -0.10 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 319 
 TYR   0.019   0.002   TYR C 316 
 PHE   0.011   0.001   PHE A 256 
 TRP   0.007   0.001   TRP B  26 
 HIS   0.003   0.001   HIS C 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01122 /  0.58 ( 7542)
  covalent geometry    : angle       1.46735 /  0.57 (10362)
  SS BOND              : bond        0.00108 /  0.06 (    2)
  SS BOND              : angle       0.24808 /  0.11 (    4)
  hydrogen bonds       : bond        0.09806 /  6.03 (  452)
  hydrogen bonds       : angle       4.46187 /  3.26 ( 1332)
  Misc. bond           : bond        0.50699 / 24.93 (    4)
  link_NAG-ASN         : bond        0.00997 /  0.50 (    2)
  link_NAG-ASN         : angle       6.57177 /  3.74 (    6)

*********************** 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
  109 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A   70 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8253 (tm-30)
REVERT: A  154 MET cc_start: 0.9008 (ptp) cc_final: 0.8654 (ptt)
REVERT: A  320 LYS cc_start: 0.8642 (mttt) cc_final: 0.8381 (mtmt)
REVERT: C   70 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8214 (tm-30)
REVERT: C  154 MET cc_start: 0.9132 (ptp) cc_final: 0.8779 (ptt)
  outliers start: 7
  outliers final: 2
  residues processed: 105
  average time/residue: 0.4154
  time to fit residues: 46.2822
Evaluate side-chains
  97 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 GLU
Chi-restraints excluded: chain C residue  155 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    1.5986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.127347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.095751 restraints weight = 8761.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 1.78
r_work: 0.3103 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.1037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   7550  Z= 0.201
  Angle     :  0.668  14.766  10372  Z= 0.302
  Chirality :  0.045   0.528   1304
  Planarity :  0.005   0.055   1006
  Dihedral  : 14.609 178.277   3702
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 13.44 %
    Favored  : 83.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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:  3.36 (0.30), residues: 738
  helix:  2.87 (0.20), residues: 558
  sheet:  None (None), residues: 0
  loop :  0.10 (0.51), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 319 
 TYR   0.015   0.002   TYR A 187 
 PHE   0.012   0.002   PHE A 256 
 TRP   0.008   0.001   TRP D  26 
 HIS   0.003   0.001   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00454 /  0.20 ( 7542)
  covalent geometry    : angle       0.63183 /  0.29 (10362)
  SS BOND              : bond        0.00109 /  0.05 (    2)
  SS BOND              : angle       0.66207 /  0.32 (    4)
  hydrogen bonds       : bond        0.06672 /  4.38 (  452)
  hydrogen bonds       : angle       4.07387 /  3.01 ( 1332)
  Misc. bond           : bond        0.00111 /  0.06 (    4)
  link_NAG-ASN         : bond        0.00667 /  0.34 (    2)
  link_NAG-ASN         : angle       9.00908 /  5.06 (    6)

*********************** 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
  123 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A   70 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7960 (tm-30)
REVERT: A  320 LYS cc_start: 0.8431 (mttt) cc_final: 0.8118 (mtmt)
REVERT: C   50 GLU cc_start: 0.8117 (mp0) cc_final: 0.7909 (mp0)
REVERT: C   70 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7961 (tm-30)
REVERT: C  154 MET cc_start: 0.9088 (ptp) cc_final: 0.8611 (ptt)
REVERT: C  171 LEU cc_start: 0.8208 (mt) cc_final: 0.7910 (mm)
REVERT: C  231 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7786 (mp)
  outliers start: 18
  outliers final: 3
  residues processed: 111
  average time/residue: 0.3844
  time to fit residues: 45.3509
Evaluate side-chains
  99 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain C residue   19 LEU
Chi-restraints excluded: chain C residue  231 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0570
   chunk 34 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   overall best weight:    0.5898

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 178 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.131494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.100075 restraints weight = 8525.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 1.77
r_work: 0.3174 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.1231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   7550  Z= 0.122
  Angle     :  0.545   6.480  10372  Z= 0.249
  Chirality :  0.039   0.389   1304
  Planarity :  0.004   0.051   1006
  Dihedral  : 13.475 157.125   3698
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.94 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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:  3.68 (0.31), residues: 738
  helix:  3.18 (0.20), residues: 552
  sheet:  None (None), residues: 0
  loop :  0.02 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 241 
 TYR   0.016   0.001   TYR C 123 
 PHE   0.008   0.001   PHE C 127 
 TRP   0.008   0.001   TRP B  26 
 HIS   0.002   0.000   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.12 ( 7542)
  covalent geometry    : angle       0.53311 /  0.25 (10362)
  SS BOND              : bond        0.00023 /  0.01 (    2)
  SS BOND              : angle       0.13753 /  0.08 (    4)
  hydrogen bonds       : bond        0.05384 /  3.51 (  452)
  hydrogen bonds       : angle       3.75184 /  2.78 ( 1332)
  Misc. bond           : bond        0.00018 /  0.01 (    4)
  link_NAG-ASN         : bond        0.01067 /  0.54 (    2)
  link_NAG-ASN         : angle       4.84717 /  2.67 (    6)

*********************** 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
  115 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8346 (tp30)
REVERT: A   70 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7854 (tm-30)
REVERT: B   31 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7300 (mt-10)
REVERT: C   20 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8370 (tp30)
REVERT: C   50 GLU cc_start: 0.8156 (mp0) cc_final: 0.7871 (mp0)
REVERT: C   70 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7826 (tm-30)
REVERT: C  154 MET cc_start: 0.9103 (ptp) cc_final: 0.8571 (ptt)
REVERT: C  171 LEU cc_start: 0.8272 (mt) cc_final: 0.7964 (mm)
  outliers start: 13
  outliers final: 6
  residues processed: 107
  average time/residue: 0.3725
  time to fit residues: 42.6839
Evaluate side-chains
  105 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain B residue   31 GLU
Chi-restraints excluded: chain C residue  164 CYS
Chi-restraints excluded: chain C residue  328 THR
Chi-restraints excluded: chain D residue   58 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 61 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   chunk 55 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    1.2182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 178 GLN
C 178 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.128268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.096557 restraints weight = 8779.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 1.79
r_work: 0.3105 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.1407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   7550  Z= 0.160
  Angle     :  0.571   8.921  10372  Z= 0.262
  Chirality :  0.043   0.521   1304
  Planarity :  0.004   0.048   1006
  Dihedral  : 13.234 157.135   3698
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 15.78 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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:  3.61 (0.30), residues: 738
  helix:  3.10 (0.20), residues: 552
  sheet:  None (None), residues: 0
  loop :  0.09 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 146 
 TYR   0.015   0.002   TYR C 123 
 PHE   0.009   0.001   PHE C 127 
 TRP   0.008   0.001   TRP D  26 
 HIS   0.002   0.000   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.16 ( 7542)
  covalent geometry    : angle       0.55225 /  0.26 (10362)
  SS BOND              : bond        0.00014 /  0.01 (    2)
  SS BOND              : angle       0.44835 /  0.21 (    4)
  hydrogen bonds       : bond        0.06003 /  3.93 (  452)
  hydrogen bonds       : angle       3.89179 /  2.87 ( 1332)
  Misc. bond           : bond        0.00052 /  0.03 (    4)
  link_NAG-ASN         : bond        0.01084 /  0.55 (    2)
  link_NAG-ASN         : angle       6.05692 /  3.41 (    6)

*********************** 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
  116 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8366 (tp30)
REVERT: A   70 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8043 (tm-30)
REVERT: B   31 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7811 (mm-30)
REVERT: C   20 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8389 (tp30)
REVERT: C   50 GLU cc_start: 0.8247 (mp0) cc_final: 0.8034 (mp0)
REVERT: C   70 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8019 (tm-30)
REVERT: C  154 MET cc_start: 0.9175 (ptp) cc_final: 0.8628 (ptt)
REVERT: C  171 LEU cc_start: 0.8361 (mt) cc_final: 0.8057 (mm)
  outliers start: 18
  outliers final: 11
  residues processed: 104
  average time/residue: 0.3748
  time to fit residues: 41.6724
Evaluate side-chains
  109 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain B residue   31 GLU
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain C residue  153 MET
Chi-restraints excluded: chain C residue  164 CYS
Chi-restraints excluded: chain C residue  328 THR
Chi-restraints excluded: chain D residue   58 SER
Chi-restraints excluded: chain D residue   62 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.7580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.130641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.099585 restraints weight = 8656.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.77
r_work: 0.3138 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7550  Z= 0.125
  Angle     :  0.523   6.643  10372  Z= 0.242
  Chirality :  0.037   0.293   1304
  Planarity :  0.004   0.046   1006
  Dihedral  : 12.703 158.592   3698
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 16.25 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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:  3.74 (0.30), residues: 738
  helix:  3.19 (0.20), residues: 552
  sheet:  None (None), residues: 0
  loop :  0.15 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 241 
 TYR   0.016   0.001   TYR C 123 
 PHE   0.008   0.001   PHE C 127 
 TRP   0.008   0.001   TRP B  26 
 HIS   0.001   0.000   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.13 ( 7542)
  covalent geometry    : angle       0.51273 /  0.24 (10362)
  SS BOND              : bond        0.00006 /  0.00 (    2)
  SS BOND              : angle       0.20978 /  0.11 (    4)
  hydrogen bonds       : bond        0.05382 /  3.51 (  452)
  hydrogen bonds       : angle       3.75754 /  2.78 ( 1332)
  Misc. bond           : bond        0.00027 /  0.01 (    4)
  link_NAG-ASN         : bond        0.00859 /  0.43 (    2)
  link_NAG-ASN         : angle       4.33074 /  2.38 (    6)

*********************** 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
  115 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8349 (tp30)
REVERT: A   70 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7935 (tm-30)
REVERT: C   20 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8345 (tp30)
REVERT: C   50 GLU cc_start: 0.8168 (mp0) cc_final: 0.7889 (mp0)
REVERT: C   70 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7914 (tm-30)
REVERT: C  154 MET cc_start: 0.9193 (ptp) cc_final: 0.8720 (ptt)
REVERT: C  171 LEU cc_start: 0.8316 (mt) cc_final: 0.8032 (mm)
  outliers start: 17
  outliers final: 6
  residues processed: 106
  average time/residue: 0.3724
  time to fit residues: 42.2585
Evaluate side-chains
  103 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  164 CYS
Chi-restraints excluded: chain C residue  328 THR
Chi-restraints excluded: chain D residue   58 SER
Chi-restraints excluded: chain D residue   62 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 13 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 70 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    1.0786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 178 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.128761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.097470 restraints weight = 8681.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.77
r_work: 0.3132 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7550  Z= 0.149
  Angle     :  0.544   6.589  10372  Z= 0.253
  Chirality :  0.038   0.264   1304
  Planarity :  0.004   0.044   1006
  Dihedral  : 12.520 157.524   3698
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 15.94 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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:  3.71 (0.30), residues: 738
  helix:  3.14 (0.20), residues: 552
  sheet:  None (None), residues: 0
  loop :  0.28 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  29 
 TYR   0.016   0.001   TYR C 123 
 PHE   0.009   0.001   PHE C 127 
 TRP   0.009   0.001   TRP B  26 
 HIS   0.001   0.000   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.15 ( 7542)
  covalent geometry    : angle       0.53766 /  0.25 (10362)
  SS BOND              : bond        0.00083 /  0.04 (    2)
  SS BOND              : angle       0.34597 /  0.15 (    4)
  hydrogen bonds       : bond        0.05860 /  3.84 (  452)
  hydrogen bonds       : angle       3.80584 /  2.82 ( 1332)
  Misc. bond           : bond        0.00035 /  0.02 (    4)
  link_NAG-ASN         : bond        0.00533 /  0.27 (    2)
  link_NAG-ASN         : angle       3.37355 /  1.85 (    6)

*********************** 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
  124 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8387 (tp30)
REVERT: A   44 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7179 (mtp180)
REVERT: A   70 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7995 (tm-30)
REVERT: A  320 LYS cc_start: 0.8376 (mttt) cc_final: 0.8116 (mtmt)
REVERT: C   20 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8371 (tp30)
REVERT: C   44 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7216 (mtp180)
REVERT: C   50 GLU cc_start: 0.8178 (mp0) cc_final: 0.7975 (mp0)
REVERT: C   70 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7968 (tm-30)
REVERT: C  171 LEU cc_start: 0.8334 (mt) cc_final: 0.8047 (mm)
REVERT: C  231 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7861 (mp)
  outliers start: 22
  outliers final: 11
  residues processed: 115
  average time/residue: 0.4291
  time to fit residues: 52.4127
Evaluate side-chains
  110 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   44 ARG
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain C residue   44 ARG
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  328 THR
Chi-restraints excluded: chain D residue   58 SER
Chi-restraints excluded: chain D residue   62 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 178 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.130246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.098725 restraints weight = 8627.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 1.77
r_work: 0.3182 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7550  Z= 0.130
  Angle     :  0.537   6.484  10372  Z= 0.247
  Chirality :  0.039   0.405   1304
  Planarity :  0.004   0.041   1006
  Dihedral  : 12.314 157.603   3698
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.81 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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:  3.76 (0.30), residues: 738
  helix:  3.17 (0.20), residues: 552
  sheet:  None (None), residues: 0
  loop :  0.30 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 146 
 TYR   0.016   0.001   TYR C 123 
 PHE   0.008   0.001   PHE C 127 
 TRP   0.009   0.001   TRP B  26 
 HIS   0.001   0.000   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.13 ( 7542)
  covalent geometry    : angle       0.52671 /  0.24 (10362)
  SS BOND              : bond        0.00060 /  0.03 (    2)
  SS BOND              : angle       0.21977 /  0.10 (    4)
  hydrogen bonds       : bond        0.05503 /  3.59 (  452)
  hydrogen bonds       : angle       3.68402 /  2.73 ( 1332)
  Misc. bond           : bond        0.00026 /  0.01 (    4)
  link_NAG-ASN         : bond        0.00551 /  0.28 (    2)
  link_NAG-ASN         : angle       4.30223 /  2.43 (    6)

*********************** 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
  118 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7192 (mtp180)
REVERT: A   70 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7987 (tm-30)
REVERT: C   44 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7223 (mtp180)
REVERT: C   50 GLU cc_start: 0.8211 (mp0) cc_final: 0.7926 (mp0)
REVERT: C   70 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7939 (tm-30)
REVERT: C  154 MET cc_start: 0.9164 (ptp) cc_final: 0.8601 (ptt)
REVERT: C  171 LEU cc_start: 0.8364 (mt) cc_final: 0.8078 (mm)
REVERT: C  231 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7885 (mp)
REVERT: D   31 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7706 (mm-30)
  outliers start: 17
  outliers final: 10
  residues processed: 112
  average time/residue: 0.4075
  time to fit residues: 48.6276
Evaluate side-chains
  111 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 ARG
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain C residue   18 LEU
Chi-restraints excluded: chain C residue   44 ARG
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  328 THR
Chi-restraints excluded: chain D residue   58 SER
Chi-restraints excluded: chain D residue   62 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0170
   chunk 3 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.5418

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.131901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.098669 restraints weight = 8931.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 1.95
r_work: 0.3049 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7550  Z= 0.115
  Angle     :  0.523   6.278  10372  Z= 0.242
  Chirality :  0.039   0.456   1304
  Planarity :  0.003   0.038   1006
  Dihedral  : 11.980 158.073   3698
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 19.06 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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:  3.87 (0.30), residues: 738
  helix:  3.25 (0.20), residues: 552
  sheet:  None (None), residues: 0
  loop :  0.35 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 149 
 TYR   0.016   0.001   TYR C 123 
 PHE   0.007   0.001   PHE C 127 
 TRP   0.009   0.001   TRP B  26 
 HIS   0.002   0.000   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.12 ( 7542)
  covalent geometry    : angle       0.51474 /  0.24 (10362)
  SS BOND              : bond        0.00036 /  0.02 (    2)
  SS BOND              : angle       0.06888 /  0.04 (    4)
  hydrogen bonds       : bond        0.05030 /  3.29 (  452)
  hydrogen bonds       : angle       3.58921 /  2.66 ( 1332)
  Misc. bond           : bond        0.00017 /  0.01 (    4)
  link_NAG-ASN         : bond        0.00227 /  0.11 (    2)
  link_NAG-ASN         : angle       3.84175 /  2.25 (    6)

*********************** 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
  118 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8299 (tp30)
REVERT: A   44 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6935 (mtp180)
REVERT: A   70 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7475 (tm-30)
REVERT: C   20 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8360 (tp30)
REVERT: C   44 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6953 (mtp180)
REVERT: C   50 GLU cc_start: 0.7829 (mp0) cc_final: 0.7571 (mp0)
REVERT: C   70 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7458 (tm-30)
REVERT: C  154 MET cc_start: 0.8963 (ptp) cc_final: 0.8320 (ptt)
REVERT: C  171 LEU cc_start: 0.8155 (mt) cc_final: 0.7845 (mm)
REVERT: D   31 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7633 (mm-30)
  outliers start: 14
  outliers final: 10
  residues processed: 113
  average time/residue: 0.3807
  time to fit residues: 45.8612
Evaluate side-chains
  111 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 ARG
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain C residue   44 ARG
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue  164 CYS
Chi-restraints excluded: chain C residue  328 THR
Chi-restraints excluded: chain D residue   58 SER
Chi-restraints excluded: chain D residue   62 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0060
   chunk 1 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.6196

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 178 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.130614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.097188 restraints weight = 8811.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 1.92
r_work: 0.3079 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7550  Z= 0.122
  Angle     :  0.571   8.664  10372  Z= 0.259
  Chirality :  0.047   0.768   1304
  Planarity :  0.004   0.036   1006
  Dihedral  : 11.808 157.814   3698
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.81 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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:  3.78 (0.30), residues: 738
  helix:  3.15 (0.20), residues: 558
  sheet:  None (None), residues: 0
  loop :  0.34 (0.51), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 149 
 TYR   0.016   0.001   TYR C 123 
 PHE   0.008   0.001   PHE C 127 
 TRP   0.010   0.001   TRP B  26 
 HIS   0.001   0.000   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.12 ( 7542)
  covalent geometry    : angle       0.54909 /  0.25 (10362)
  SS BOND              : bond        0.00020 /  0.01 (    2)
  SS BOND              : angle       0.08827 /  0.03 (    4)
  hydrogen bonds       : bond        0.05153 /  3.37 (  452)
  hydrogen bonds       : angle       3.57962 /  2.66 ( 1332)
  Misc. bond           : bond        0.00021 /  0.01 (    4)
  link_NAG-ASN         : bond        0.00693 /  0.35 (    2)
  link_NAG-ASN         : angle       6.61085 /  3.85 (    6)

*********************** 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
  113 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8230 (tp30)
REVERT: A   44 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6912 (mtp180)
REVERT: A   70 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7392 (tm-30)
REVERT: C   20 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8285 (tp30)
REVERT: C   44 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6890 (mtp180)
REVERT: C   50 GLU cc_start: 0.7776 (mp0) cc_final: 0.7510 (mp0)
REVERT: C   70 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7330 (tm-30)
REVERT: C  154 MET cc_start: 0.8918 (ptp) cc_final: 0.8391 (ptt)
REVERT: C  171 LEU cc_start: 0.8116 (mt) cc_final: 0.7801 (mm)
REVERT: D   31 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7548 (mm-30)
  outliers start: 17
  outliers final: 12
  residues processed: 108
  average time/residue: 0.3861
  time to fit residues: 44.4719
Evaluate side-chains
  110 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 ARG
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain C residue   44 ARG
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  164 CYS
Chi-restraints excluded: chain C residue  328 THR
Chi-restraints excluded: chain D residue   58 SER
Chi-restraints excluded: chain D residue   62 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 50 optimal weight:    0.3980
   chunk 61 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.9382

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.127969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.094285 restraints weight = 8869.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 1.93
r_work: 0.3034 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2889 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
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      :  0.003   0.030   7550  Z= 0.142
  Angle     :  0.577   7.006  10372  Z= 0.267
  Chirality :  0.043   0.574   1304
  Planarity :  0.004   0.038   1006
  Dihedral  : 11.892 156.737   3698
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 18.12 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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:  3.71 (0.30), residues: 738
  helix:  3.12 (0.20), residues: 552
  sheet:  None (None), residues: 0
  loop :  0.35 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 149 
 TYR   0.016   0.001   TYR C 123 
 PHE   0.010   0.001   PHE C 127 
 TRP   0.009   0.001   TRP B  26 
 HIS   0.001   0.000   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 ( 7542)
  covalent geometry    : angle       0.56328 /  0.26 (10362)
  SS BOND              : bond        0.00037 /  0.02 (    2)
  SS BOND              : angle       0.23393 /  0.10 (    4)
  hydrogen bonds       : bond        0.05755 /  3.76 (  452)
  hydrogen bonds       : angle       3.70284 /  2.75 ( 1332)
  Misc. bond           : bond        0.00036 /  0.02 (    4)
  link_NAG-ASN         : bond        0.00811 /  0.41 (    2)
  link_NAG-ASN         : angle       5.20195 /  3.00 (    6)

********************** 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
  115 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A   20 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8160 (tp30)
REVERT: A   44 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6922 (mtp180)
REVERT: A   70 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7481 (tm-30)
REVERT: C   20 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8199 (tp30)
REVERT: C   44 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6922 (mtp180)
REVERT: C   50 GLU cc_start: 0.7760 (mp0) cc_final: 0.7477 (mp0)
REVERT: C   70 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7418 (tm-30)
REVERT: C   76 TYR cc_start: 0.8744 (t80) cc_final: 0.8543 (t80)
REVERT: C  154 MET cc_start: 0.8898 (ptp) cc_final: 0.8356 (ptt)
REVERT: C  171 LEU cc_start: 0.8101 (mt) cc_final: 0.7791 (mm)
REVERT: C  231 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7215 (mp)
REVERT: D   31 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7472 (mm-30)
  outliers start: 16
  outliers final: 11
  residues processed: 111
  average time/residue: 0.3713
  time to fit residues: 44.0326
Evaluate side-chains
  108 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 ARG
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  164 CYS
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain C residue   44 ARG
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  164 CYS
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  328 THR
Chi-restraints excluded: chain D residue   58 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 15 optimal weight:    0.1980
   chunk 64 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.9984

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.128116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.094654 restraints weight = 8918.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 1.93
r_work: 0.3034 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2889 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7550  Z= 0.146
  Angle     :  0.575   7.353  10372  Z= 0.268
  Chirality :  0.039   0.502   1304
  Planarity :  0.004   0.038   1006
  Dihedral  : 11.907 156.710   3698
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 18.44 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.00 %
    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:  3.67 (0.30), residues: 738
  helix:  3.07 (0.20), residues: 552
  sheet:  None (None), residues: 0
  loop :  0.39 (0.50), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 149 
 TYR   0.016   0.002   TYR C 123 
 PHE   0.009   0.001   PHE C 127 
 TRP   0.008   0.001   TRP B  26 
 HIS   0.001   0.000   HIS A 156 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.15 ( 7542)
  covalent geometry    : angle       0.56333 /  0.26 (10362)
  SS BOND              : bond        0.00049 /  0.03 (    2)
  SS BOND              : angle       0.23612 /  0.10 (    4)
  hydrogen bonds       : bond        0.05712 /  3.74 (  452)
  hydrogen bonds       : angle       3.69027 /  2.74 ( 1332)
  Misc. bond           : bond        0.00035 /  0.02 (    4)
  link_NAG-ASN         : bond        0.00577 /  0.29 (    2)
  link_NAG-ASN         : angle       4.87839 /  2.68 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1966.15 seconds
wall clock time: 34 minutes 16.22 seconds (2056.22 seconds total)